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@comment{jabref-meta: selector_journal:Computer Aided Geometric Design ;Computer Graphics;Computer Vision and Image Understanding;IEEE Comput er Graphics and Applications;IEEE Transactions on Image Processing;IEE E Transactions on Medical Imaging;IEEE Transactions on Pattern Analysi s and Machine Intelligence;IEEE Transactions on Visualization and Comp uter Graphics;Insight Journal;International Journal of Computer Vision ;Journal of Mathematical Imaging and Vision;Medical Image Analysis;SIA M Journal of Applied Mathematics;}



@article{Avants:2010aa,
	Abstract = {We present a new algorithm for reliable, unbiased, multivariate longitudinal analysis of cortical and white matter atrophy rates with penalized statistical methods. The pipeline uses a step-wise approach to transform and personalize template information first to a single-subject template (SST) and then to the individual's time series data. The first stream of information flows from group template to the SST; the second flows from the SST to the individual time-points and provides unbiased, prior-based segmentation and measurement of cortical thickness. MRI-bias correction, consistent longitudinal segmentation, cortical parcellation and cortical thickness estimation are all based on strong use of the subject-specific priors built from initial diffeomorphic mapping between the SST and optimal group template. We evaluate our approach with both test-retest data and with application to a driving biological problem. We use test-retest data to show that this approach produces (a) zero change when the retest data contains the same image content as the test data and (b) produces normally distributed, low variance estimates of thickness change centered at zero when test-retest data is collected near in time to test data. We also show that our approach--when combined with sparse canonical correlation analysis--reveals plausible, significant, annualized decline in cortical thickness and white matter volume when contrasting frontotemporal dementia and normal aging.},
	Author = {Avants, Brian and Cook, Philip A and McMillan, Corey and Grossman, Murray and Tustison, Nicholas J and Zheng, Yuanjie and Gee, James C},
	Date-Added = {2014-05-15 23:09:01 +0000},
	Date-Modified = {2014-05-15 23:09:01 +0000},
	Journal = {Med Image Comput Comput Assist Interv},
	Journal-Full = {Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention},
	Mesh = {Algorithms; Analysis of Variance; Brain; Brain Diseases; Humans; Image Enhancement; Image Interpretation, Computer-Assisted; Longitudinal Studies; Magnetic Resonance Imaging; Pattern Recognition, Automated; Prognosis; Reproducibility of Results; Sensitivity and Specificity; Subtraction Technique},
	Number = {Pt 1},
	Pages = {324-31},
	Pmc = {PMC3641640},
	Pmid = {20879247},
	Pst = {ppublish},
	Title = {Sparse unbiased analysis of anatomical variance in longitudinal imaging},
	Volume = {13},
	Year = {2010}}

@article{Avants:2014aa,
	Abstract = {Publicly available scientific resources help establish evaluation standards, provide a platform for teaching and improve reproducibility. Version 4 of the Insight ToolKit (ITK(4)) seeks to establish new standards in publicly available image registration methodology. ITK(4) makes several advances in comparison to previous versions of ITK. ITK(4) supports both multivariate images and objective functions; it also unifies high-dimensional (deformation field) and low-dimensional (affine) transformations with metrics that are reusable across transform types and with composite transforms that allow arbitrary series of geometric mappings to be chained together seamlessly. Metrics and optimizers take advantage of multi-core resources, when available. Furthermore, ITK(4) reduces the parameter optimization burden via principled heuristics that automatically set scaling across disparate parameter types (rotations vs. translations). A related approach also constrains steps sizes for gradient-based optimizers. The result is that tuning for different metrics and/or image pairs is rarely necessary allowing the researcher to more easily focus on design/comparison of registration strategies. In total, the ITK(4) contribution is intended as a structure to support reproducible research practices, will provide a more extensive foundation against which to evaluate new work in image registration and also enable application level programmers a broad suite of tools on which to build. Finally, we contextualize this work with a reference registration evaluation study with application to pediatric brain labeling.},
	Author = {Avants, Brian B and Tustison, Nicholas J and Stauffer, Michael and Song, Gang and Wu, Baohua and Gee, James C},
	Date-Added = {2014-05-15 23:07:14 +0000},
	Date-Modified = {2014-05-15 23:07:14 +0000},
	Doi = {10.3389/fninf.2014.00044},
	Journal = {Front Neuroinform},
	Journal-Full = {Frontiers in neuroinformatics},
	Keywords = {MRI; brain; death; open-source; registration},
	Pages = {44},
	Pmid = {24817849},
	Pst = {epublish},
	Title = {The Insight ToolKit image registration framework},
	Volume = {8},
	Year = {2014},
	Bdsk-Url-1 = {http://dx.doi.org/10.3389/fninf.2014.00044}}

@article{Agarwal2006,
	Author = {Agarwal, A. and Triggs, B.},
	Doi = {10.1109/TPAMI.2006.21},
	Journal = IEEE_J_PAMI,
	Month = {Jan.},
	Number = {1},
	Pages = {44--58},
	Timestamp = {2008.11.26},
	Title = {Recovering 3D human pose from monocular images},
	Volume = {28},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2006.21}}

@article{Alexander2001,
	Author = {DC Alexander and C Pierpaoli and PJ Basser and JC Gee},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Adult, Algorithms, Automation, Brain, Comparative Study, Diffusion, Fourier Analysis, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Models, Theoretical, Reference Values, Research Support, U.S. Gov't, P.H.S., 11700739},
	Month = {Nov},
	Number = {11},
	Owner = {tustison},
	Pages = {1131-9},
	Title = {Spatial transformations of diffusion tensor magnetic resonance images.},
	Volume = {20},
	Year = {2001}}

@article{Alexander2000,
	Author = {Daniel C. Alexander and James C. Gee},
	Journal = {Computer Vision and Image Understanding},
	Number = {77},
	Owner = {tustison},
	Pages = {233-250},
	Title = {Elastic Matching of Diffusion Tensor Images},
	Year = {2000}}

@article{Allen2002,
	Abstract = {Normative data on the in vivo size of the human brain and its major anatomically defined subdivisions are not readily available. In this study, high-resolution magnetic resonance imaging was used to measure regional brain volumes in 46 normal, right-handed adults (23 men, 23 women) between the ages of 22-49 years. Parcellation of the brain was based on neuroanatomical landmarks. The following brain regions were measured: the cerebral hemispheres, frontal lobe, temporal lobe, parietal lobe, occipital lobe, cingulate gyrus, insula, cerebellum, corpus callosum, and lateral ventricles. Males tend to be significantly larger than females, for the whole brain and for nearly all of its major subdivisions, including the corpus callosum. However, the proportional sizes of regions relative to total volume of the hemisphere are remarkably similar in males and females. Variation in size of region is always greater than variation in proportional representation. Asymmetries in brain regions are not profound, with the exception of the cingulate gyrus, which is larger in the left hemisphere. Brain regions are highly correlated in size, with the exception of the lateral ventricles. After controlling for hemisphere size, the volumes of the frontal and parietal lobes are significantly negatively correlated. The occipital lobe tends to be less sexually dimorphic than other major lobes, and less correlated with other brain regions for volume. These results have implications for understanding whether or not certain sectors of the brain have shown relative expansion over the course of hominid and hominoid evolution.},
	Author = {John S Allen and Hanna Damasio and Thomas J Grabowski},
	Doi = {10.1002/ajpa.10092},
	Institution = {Division of Behavioral Neurology and Cognitive Neuroscience, Department of Neurology, University of Iowa Hospitals and Clinics, Iowa City, Iowa 52242, USA. jsallen38@aol.com},
	Journal = {Am J Phys Anthropol},
	Keywords = {Adult; Brain; Female; Humans; Magnetic Resonance Imaging; Male; Middle Aged; Neuroanatomy; Sex Distribution},
	Month = {Aug},
	Number = {4},
	Pages = {341--358},
	Pmid = {12124914},
	Timestamp = {2009.06.27},
	Title = {Normal neuroanatomical variation in the human brain: an MRI-volumetric study.},
	Url = {http://dx.doi.org/10.1002/ajpa.10092},
	Volume = {118},
	Year = {2002},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/ajpa.10092}}

@article{Allen2003,
	Abstract = {Using high resolution MRI scans and automated tissue segmentation, gray and white matter (GM, WM) volumes of the frontal, temporal, parietal, and occipital lobes, cingulate gyrus, and insula were calculated. Subjects included 23 male and 23 female healthy, right-handed subjects. For all structures, male volumes were greater than female, but the gray/white (G/W) ratio was consistently higher across structures in women than men. Sexual dimorphism was greater for WM than GM: most of the G/W ratio sex differences can be attributed to variation in WM volume. The corpus callosum, although larger in men, is less sexually dimorphic than the WM as a whole. Several regions demonstrate pair-wise asymmetries in G/W ratio and WM volume. Both the cingulate gyrus and insula exhibit strong asymmetries. The left cingulate gyrus is significantly larger than the right, and the G/W ratio of the left insula is significantly greater than that of the right. Although statistically significant sex differences and asymmetries are present at this level of analysis, we argue that researchers should be wary of ascribing cognitive functional significance to these patterns at this time. This is not to say, however, that these patterns are not important for understanding the natural history of the human brain, and its evolution and development.},
	Author = {John S Allen and Hanna Damasio and Thomas J Grabowski and Joel Bruss and Wei Zhang},
	Institution = {Department of Neurology, University of Iowa Hospitals and Clinics, 200 Hawkins Drive, Iowa City, IA 52242, USA. jsallen38@aol.com},
	Journal = {Neuroimage},
	Keywords = {Adult; Brain Mapping; Female; Humans; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Male; Middle Aged; Reference Values; Sex Characteristics; Telencephalon},
	Month = {Apr},
	Number = {4},
	Pages = {880--894},
	Pii = {S105381190300034X},
	Pmid = {12725764},
	Timestamp = {2009.06.27},
	Title = {Sexual dimorphism and asymmetries in the gray-white composition of the human cerebrum.},
	Volume = {18},
	Year = {2003}}

@inproceedings{Altes2007,
	Author = {T. A. Altes and J. C. Gersback and J. F. Mata and J. P. Mugler III and J. R. Brookeman and E.E. de Lange},
	Booktitle = {Proceedings of the Scientific Meeting and Exhibition of the International Society of Magnetic Resonance Imaging},
	Timestamp = {2008.02.13},
	Title = {Evaluation of the Safety of Hyperpolarized Helium-3 Gas as an Inhaled Contrast Agent for MRI},
	Year = {2007}}

@article{Altes2001,
	Abstract = {Asthma is a disease characterized by chronic inflammation and reversible obstruction of the small airways resulting in impaired pulmonary ventilation. Hyperpolarized 3He magnetic resonance (MR) lung imaging is a new technology that provides a detailed image of lung ventilation. Hyperpolarized 3He lung imaging was performed in 10 asthmatics and 10 healthy subjects. Seven asthmatics had ventilation defects distributed throughout the lungs compared with none of the normal subjects. These ventilation defects were more numerous and larger in the two symptomatic asthmatics who had abnormal spirometry. Ventilation defects studied over time demonstrated no change in appearance over 30-60 minutes. One asthmatic subject was studied twice in a three-week period and had ventilation defects which resolved and appeared in that time. This same subject was studied before and after bronchodilator therapy, and all ventilation defects resolved after therapy. Hyperpolarized 3He lung imaging can detect the small, reversible ventilation defects that characterize asthma. The ability to visualize lung ventilation offers a direct method of assessing asthmatics and their response to therapy.},
	Author = {T. A. Altes and P. L. Powers and J. Knight-Scott and G. Rakes and T. A. Platts-Mills and E. E. de Lange and B. A. Alford and J. P. Mugler and J. R. Brookeman},
	Institution = {Department of Radiology, University of Virginia, Charlottesville, Virginia, USA. taa2c@virginia.edu},
	Journal = {J Magn Reson Imaging},
	Keywords = {Adult; Asthma; Female; Helium; Humans; Image Enhancement; Image Processing, Computer-Assisted; Isotopes; Ma; Male; Observer Variation; Pulmonary Gas Exchange; Spirometry; gnetic Resonance Imaging},
	Month = {Mar},
	Number = {3},
	Pages = {378--384},
	Pii = {10.1002/jmri.1054},
	Pmid = {11241810},
	Timestamp = {2008.01.10},
	Title = {Hyperpolarized {3He} {MR} lung ventilation imaging in asthmatics: preliminary findings.},
	Volume = {13},
	Year = {2001}}

@inproceedings{Amini1994,
	Author = {Amir A. Amini},
	Booktitle = {Lecture Notes in Computer Science, Vol. 800 Computer Vision - ECCV `94},
	Owner = {tustison},
	Pages = {125-131},
	Title = {A Scalar Function Formulation for Optical Flow},
	Year = {1994}}

@unpublished{Amini1992,
	Author = {Amir A. Amini and James S. Duncan},
	Month = {October},
	Owner = {tustison},
	Title = {Differential Goemetric Models for Non-rigid Motion},
	Year = {1992}}

@article{Amini1990,
	Author = {Amir A. Amini and Terry E. Weymouth and Ramesh C. Jain},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {9},
	Owner = {tustison},
	Pages = {855-867},
	Title = {Using Dynamic Programming for Solving Variational Problems in Vision},
	Volume = {12},
	Year = {1990}}

@article{Anandan1989,
	Author = {P. Anandan},
	Journal = {International Journal of Computer Vision},
	Owner = {tustison},
	Pages = {283-310},
	Title = {A Computational Framework and an Algorithm for the Measurement of Visual Motion},
	Volume = {2},
	Year = {1989}}

@inproceedings{Andarawis2006,
	Author = {Nelly A. Andarawis and Jane C. Asmuth and Joseph J. Sarver and Nicholas J. Tustison and Brian B. Avants and Felix W. Wehrli and James C. Gee and Louis J. Soslowsky},
	Booktitle = {Proc. of the 2006 Summer Bioengineering Conference},
	Timestamp = {2009.05.18},
	Title = {Removal of the Coracoacromial Arch Causes Alterations in Apparent Strain in the Superior Region of the Supraspinatus Tendon},
	Year = {2006}}

@article{Andresen2000,
	Abstract = {From a set of longitudinal three-dimensional scans of the same anatomical structure, we have accurately modeled the temporal shape and size changes using a linear shape model. On a total of 31 computed tomography scans of the mandible from six patients, 14,851 semilandmarks are found automatically using shape features and a new algorithm called geometry-constrained diffusion. The semilandmarks are mapped into Procrustes space. Principal component analysis extracts a one-dimensional subspace, which is used to construct a linear growth model. The worst case mean modeling error in a cross validation study is 3.7 mm.},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Anthropometry, Child, Child, Preschool, Computer Simulation, Female, Humans, Infant, Male, Mandible, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, P.H.S., 11204843},
	Month = {Nov},
	Number = {11},
	Owner = {tustison},
	Pages = {1053-63},
	Title = {Surface-bounded growth modeling applied to human mandibles.},
	Volume = {19},
	Year = {2000}}

@article{Andresen2001,
	Author = {Per Ronsholt Andresen and Mads Nielsen},
	Journal = {Medical Image Analysis},
	Owner = {tustison},
	Pages = {81-88},
	Title = {Non-rigid registration by geometry-constrained diffusion},
	Volume = {5},
	Year = {2001}}

@article{Angenent1999,
	Abstract = {In this paper, using certain conformal mappings from uniformization theory, we give an explicit method for flattening the brain surface in a way which preserves angles. From a triangulated surface representation of the cortex, we indicate how the procedure may be implemented using finite elements. Further, we show how the geometry of the brain surface may be studied using this approach.},
	Author = {S Angenent and S Haker and A Tannenbaum and R Kikinis},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Brain, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S., 10534052},
	Month = {Aug},
	Number = {8},
	Owner = {tustison},
	Pages = {700-11},
	Title = {On the {L}aplace-{B}eltrami operator and brain surface flattening.},
	Volume = {18},
	Year = {1999}}

@article{Arakawa2001,
	Author = {A. Arakawa and Y. Yamashita and Y. Nakayama and M. Kadota and H. Korogi and O. Kawano and M. Matsumoto and M. Takahashi},
	Journal = {Comput Med Imaging Graph},
	Number = {5},
	Pages = {399--404},
	Timestamp = {2009.05.18},
	Title = {Assessment of lung volumes in pulmonary emphysema using multidetector helical {CT}: comparison with pulmonary function tests.},
	Volume = {25},
	Year = {2001}}

@article{Argenti1990,
	Author = {F. Argenti and L. Alparone and G. Benelli},
	Journal = {IEE Proceedings, Part F: Radar and Signal Processing},
	Number = {6},
	Owner = {tustison},
	Pages = {443-448},
	Title = {Fast algorithms for texture analysis using co-occurrence matrices},
	Volume = {137},
	Year = {1990}}

@article{Armato2004,
	Author = {Samuel G Armato and Geoffrey McLennan and Michael F McNitt-Gray and Charles R Meyer and David Yankelevitz and Denise R Aberle and Claudia I Henschke and Eric A Hoffman and Ella A Kazerooni and Heber MacMahon and Anthony P Reeves and Barbara Y Croft and Laurence P Clarke and Lung Image Database Consortium Research Group},
	Journal = {Radiology},
	Month = {Sep},
	Number = {3},
	Pages = {739--748},
	Timestamp = {2009.05.18},
	Title = {Lung image database consortium: developing a resource for the medical imaging research community.},
	Volume = {232},
	Year = {2004}}

@book{Arnold1991,
	Author = {V. I. Arnold},
	Publisher = {Springer-Verlag},
	Timestamp = {2009.06.06},
	Title = {Ordinary Differential Equations},
	Year = {1991}}

@article{Arsigny2005,
	Author = {Vincent Arsigny and Xavier Pennec and Nicholas Ayache},
	Journal = {Medical Image Analysis},
	Owner = {tustison},
	Title = {Polyrigid and Polyaffine Transformations: a Novel Geometrical Tool to Deal with Non-Rigid Deformations. Application to the registration of histological slices.},
	Year = {2005}}

@article{Ashburner2007,
	Abstract = {This paper describes DARTEL, which is an algorithm for diffeomorphic image registration. It is implemented for both 2D and 3D image registration and has been formulated to include an option for estimating inverse consistent deformations. Nonlinear registration is considered as a local optimisation problem, which is solved using a Levenberg-Marquardt strategy. The necessary matrix solutions are obtained in reasonable time using a multigrid method. A constant Eulerian velocity framework is used, which allows a rapid scaling and squaring method to be used in the computations. DARTEL has been applied to intersubject registration of 471 whole brain images, and the resulting deformations were evaluated in terms of how well they encode the shape information necessary to separate male and female subjects and to predict the ages of the subjects.},
	Author = {John Ashburner},
	Doi = {j.neuroimage.2007.07.007},
	Institution = {Wellcome Trust Centre for Neuroimaging, 12 Queen Square, London, UK. j.ashburner@fil.ion.ac.uk},
	Journal = {Neuroimage},
	Keywords = {Algorithms; Artificial Intelligence; Brain; Humans; Image Enhancement; Image Interpretation, Computer-Assisted; Imaging, Three-Dimensional; Magnetic Resonance Imaging; Pattern Recognition, Automated; Reproduci; Sensitivity and Specificity; Subtraction Technique; bility of Results},
	Month = {Oct},
	Number = {1},
	Pages = {95--113},
	Pii = {S1053-8119(07)00584-8},
	Pmid = {17761438},
	Timestamp = {2009.06.06},
	Title = {A fast diffeomorphic image registration algorithm.},
	Url = {http://dx.doi.org/j.neuroimage.2007.07.007},
	Volume = {38},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/j.neuroimage.2007.07.007},
	Bdsk-Url-2 = {http://dx.doi.org/2007.07.007}}

@article{Ashburner1999,
	Abstract = {This paper is about warping a brain image from one subject (the object image) so that it matches another (the template image). A high-dimensional model is used, whereby a finite element approach is employed to estimate translations at the location of each voxel in the template image. Bayesian statistics are used to obtain a maximum a posteriori (MAP) estimate of the deformation field. The validity of any registration method is largely based upon the constraints or, in this instance, priors incorporated into the model describing the transformations. In this approach we assume that the priors should have some form of symmetry, in that priors describing the probability distribution of the deformations should be identical to those for the inverses (i.e., warping brain A to brain B should not be different probabilistically from warping B to A). The fundamental assumption is that the probability of stretching a voxel by a factor of n is considered to be the same as the probability of shrinking n voxels by a factor of n(-1). In the Bayesian framework adopted here, the priors are assumed to have a Gibbs form, where the Gibbs potential is a penalty function that embodies this symmetry. The penalty function of choice is based upon the singular values of the Jacobian having a lognormal distribution. This enforces a continuous one-to-one mapping. A gradient descent algorithm is presented that incorporates the above priors in order to obtain a MAP estimate of the deformations. We demonstrate this approach for the two-dimensional case, but the principles can be extended to three dimensions. A number of examples are given to demonstrate how the method works.},
	Author = {J Ashburner and JL Andersson and KJ Friston},
	Journal = {Neuroimage},
	Keywords = {Bayes Theorem, Brain Mapping, Computer Simulation, Humans, Image Processing, Computer-Assisted, Likelihood Functions, Magnetic Resonance Imaging, Probability, Research Support, Non-U.S. Gov't, Tomography, Emission-Computed, 10334905},
	Month = {Jun},
	Number = {6 Pt 1},
	Owner = {tustison},
	Pages = {619-28},
	Pii = {S1053811999904378},
	Title = {High-dimensional image registration using symmetric priors.},
	Volume = {9},
	Year = {1999}}

@article{Ashburner2000,
	Author = {J. Ashburner and K. Friston},
	Journal = {Neuroimage},
	Pages = {805-821},
	Title = {Voxel-based morphometry---{The} methods},
	Volume = {11},
	Year = {2000}}

@article{Aslan2008,
	Author = {Aslan, Cagri and Erdem, Aykut and Erdem, Erkut and Tari, Sibel},
	Doi = {10.1109/TPAMI.2007.70842},
	Journal = IEEE_J_PAMI,
	Month = {Dec.},
	Number = {12},
	Pages = {2188--2203},
	Timestamp = {2008.11.26},
	Title = {Disconnected Skeleton: Shape at Its Absolute Scale},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70842}}

@inproceedings{Asmuth2006,
	Author = {J. C. Asmuth and N. A. Andarawis and N. J. Tustison and B. B. Avants and J. J. Sarver and L. J. Soslowsky and J. C. Gee},
	Booktitle = {Proc. of the 14th Annual Meeting of ISMRM},
	Timestamp = {2009.05.18},
	Title = {Robust Method to Measure Tendon Strain},
	Year = {2006}}

@article{Avants2007b,
	Author = {Brian Avants and Chivon Anderson and Murray Grossman and James C Gee},
	Journal = {Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv},
	Number = {Pt 2},
	Pages = {303--310},
	Timestamp = {2009.05.18},
	Title = {Spatiotemporal normalization for longitudinal analysis of gray matter atrophy in frontotemporal dementia.},
	Volume = {10},
	Year = {2007}}

@article{Avants2004,
	Author = {Brian Avants and James C Gee},
	Journal = {Neuroimage},
	Pages = {S139--S150},
	Timestamp = {2009.05.18},
	Title = {Geodesic estimation for large deformation anatomical shape averaging and interpolation.},
	Volume = {23 Suppl 1},
	Year = {2004}}

@article{Avants2005,
	Author = {Brian Avants and Murray Grossman and James C Gee},
	Journal = {Alzheimer Dis Assoc Disord},
	Pages = {S25--S28},
	Timestamp = {2009.05.18},
	Title = {The correlation of cognitive decline with frontotemporal dementia induced annualized gray matter loss using diffeomorphic morphometry.},
	Volume = {19 Suppl 1},
	Year = {2005}}

@inbook{Avants2004a,
	Author = {Brian Avants and Tessa Sundaram and Jeffrey T. Duda and James C. Gee and Lydia Ng},
	Chapter = {Non-Rigid Image Registration},
	Editor = {Terry S. Yoo},
	Owner = {tustison},
	Pages = {307-348},
	Publisher = {A K Peters},
	Timestamp = {2009.05.18},
	Title = {Insight into Images},
	Year = {2004}}

@inbook{Avants,
	Author = {Brian B. Avants and C. L. Epstein and J. C. Gee},
	Chapter = {Geodesic Image Interpolation: Parameterizing and Interpolating Spatiotemporal Images},
	Owner = {tustison}}

@article{Avants2007,
	Author = {Brian B. Avants and Charles L. Epstein and James C. Gee},
	Journal = {Transactions on Medical Imaging},
	Timestamp = {2007.03.15},
	Title = {Symmetric Image Normalization and Temporal Parameterization in the Space of Diffeomorphisms},
	Year = {2007}}

@inbook{Avantsa,
	Author = {Brian B. Avants and C. L. Epstein and J. C. Gee},
	Chapter = {Geodesic Image Interpolation: Parameterizing and Interpolating Spatiotemporal Images},
	Owner = {tustison},
	Pages = {247-258},
	Publisher = {Springer Berlin / Heidelberg},
	Series = {Lecture Notes In Computer Science},
	Timestamp = {2009.05.18},
	Title = {Variational, Geometric, and Level Set Methods in Computer Vision},
	Volume = {3752},
	Year = {2005}}

@article{Avants2008,
	Author = {B. B. Avants and C. L. Epstein and M. Grossman and J. C. Gee},
	Journal = {Med Image Anal},
	Month = {Feb},
	Number = {1},
	Pages = {26--41},
	Timestamp = {2009.05.18},
	Title = {Symmetric diffeomorphic image registration with cross-correlation: evaluating automated labeling of elderly and neurodegenerative brain.},
	Volume = {12},
	Year = {2008}}

@inproceedings{Avants2003,
	Author = {Brian B. Avants and James C. Gee},
	Bibsource = {DBLP, http://dblp.uni-trier.de},
	Booktitle = {Workshop on Biomedical Image Registration},
	Ee = {http://springerlink.metapress.com/openurl.asp?genre=article{\&}issn=0302-9743{\&} volume=2717{\&}spage=21},
	Pages = {21-30},
	Timestamp = {2009.05.18},
	Title = {Formulation and Evaluation of Variational Curve Matching with Prior Constraints.},
	Year = {2003}}

@article{Avants2007a,
	Author = {Brian B Avants and Hallam Hurt and Joan M Giannetta and Charles L Epstein and David M Shera and Hengyi Rao and Jiongjiong Wang and James C Gee},
	Journal = {Pediatr Neurol},
	Month = {Oct},
	Number = {4},
	Pages = {275--279},
	Timestamp = {2009.05.18},
	Title = {Effects of heavy in utero cocaine exposure on adolescent caudate morphology.},
	Volume = {37},
	Year = {2007}}

@article{Avants2006,
	Author = {Brian B Avants and P. Thomas Schoenemann and James C Gee},
	Journal = {Med Image Anal},
	Month = {Jun},
	Number = {3},
	Pages = {397--412},
	Timestamp = {2009.05.18},
	Title = {Lagrangian frame diffeomorphic image registration: Morphometric comparison of human and chimpanzee cortex.},
	Volume = {10},
	Year = {2006}}

@manual{ANTS2009,
	Author = {Brian B. Avants and Nicholas J. Tustison and Gang Song and James C. Gee},
	Organization = {Penn Image Computing and Science Laboratory},
	Timestamp = {2009.03.09},
	Title = {ANTS: Advanced Open-Source Normalization Tools for Neuroanatomy},
	Url = {http://www.picsl.upenn.edu/ANTS},
	Year = {2009},
	Bdsk-Url-1 = {http://www.picsl.upenn.edu/ANTS}}

@book{Avriel1976,
	Author = {Mordecai Avriel},
	Publisher = {Englewood Cliffs, N.J. : Prentice-Hall},
	Timestamp = {2007.06.19},
	Title = {Nonlinear programming : analysis and methods},
	Year = {1976}}

@article{Awate2006,
	Abstract = {This paper presents a novel method for brain-tissue classification in magnetic resonance (MR) images that relies on a very general, adaptive statistical model of image neighborhoods. The method models MR-tissue intensities as derived from stationary random fields. It models the associated Markov statistics nonparametrically via a data-driven strategy. This paper describes the essential theoretical aspects underpinning adaptive, nonparametric Markov modeling and the theory behind the consistency of such a model. This general formulation enables the method to easily adapt to various kinds of MR images and the associated acquisition artifacts. It implicitly accounts for the intensity nonuniformity and performs reasonably well on T1-weighted MR data without nonuniformity correction. The method minimizes an information-theoretic metric on the probability density functions associated with image neighborhoods to produce an optimal classification. It automatically tunes its important internal parameters based on the information content of the data. Combined with an atlas-based initialization, it is completely automatic. Experiments on real, simulated, and multimodal data demonstrate the advantages of the method over the current state-of-the-art.},
	Author = {Suyash P Awate and Tolga Tasdizen and Norman Foster and Ross T Whitaker},
	Doi = {10.1016/j.media.2006.07.002},
	Institution = {School of Computing, Scientific Computing and Imaging Institute, University of Utah, 50 South Central Campus Drive, Salt Lake City, UT 84112, USA. suyash@cs.utah.edu},
	Journal = {Med Image Anal},
	Keywords = {Algorithms; Artificial Intelligence; Brain; Computer Simulation; Humans; Image Enhancement; Image Interpretation, Computer-Assisted; Magnetic Resonance Imaging; Markov Ch; Models, Neurological; Models, Statistical; Pattern Recognition, Automated; Reproducibility of Results; Sensitivity and Specificity; ains},
	Month = {Oct},
	Number = {5},
	Pages = {726--739},
	Pii = {S1361-8415(06)00056-9},
	Pmid = {16919993},
	Timestamp = {2009.03.27},
	Title = {Adaptive Markov modeling for mutual-information-based, unsupervised MRI brain-tissue classification.},
	Url = {http://dx.doi.org/10.1016/j.media.2006.07.002},
	Volume = {10},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.media.2006.07.002}}

@article{Awate2007,
	Author = {Suyash P Awate and Hui Zhang and James C Gee},
	Journal = {IEEE Trans Med Imaging},
	Month = {Nov},
	Number = {11},
	Pages = {1525--1536},
	Timestamp = {2009.05.18},
	Title = {A fuzzy, nonparametric segmentation framework for {DTI} and {MRI} analysis: with applications to {DTI}-tract extraction.},
	Volume = {26},
	Year = {2007}}

@article{Axel1989,
	Author = {L. Axel and L. Dougherty},
	Journal = {Radiology},
	Pages = {841-845},
	Timestamp = {2006.12.20},
	Title = {{MR} Imaging of Motion with Spatial Modulation of Magnetization},
	Volume = {171},
	Year = {1989}}

@article{Aykac2003,
	Author = {Deniz Aykac and Eric A Hoffman and Geoffrey McLennan and Joseph M Reinhardt},
	Journal = {IEEE Trans Med Imaging},
	Month = {Aug},
	Number = {8},
	Pages = {940--950},
	Timestamp = {2009.05.18},
	Title = {Segmentation and analysis of the human airway tree from three-dimensional {X}-ray {CT} images.},
	Volume = {22},
	Year = {2003}}

@article{Bai2008,
	Author = {Xiang Bai and Latecki, L.J.},
	Doi = {10.1109/TPAMI.2007.70769},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Month = {July},
	Number = {7},
	Pages = {1282--1292},
	Timestamp = {2008.11.26},
	Title = {Path Similarity Skeleton Graph Matching},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70769}}

@inproceedings{Bajcsy1982,
	Author = {Ruzena Bajcsy and Chaim Broit},
	Booktitle = {International Conference on Pattern Recognition},
	Owner = {tustison},
	Title = {Matching of deformed images},
	Year = {1982}}

@article{Bajcsy1989,
	Author = {Ruzena Bajcsy and Stane Kovacic},
	Journal = {Computer Vision, Graphics, and Image Processing},
	Owner = {tustison},
	Pages = {1-21},
	Title = {Multiresolution Elastic Matching},
	Volume = {46},
	Year = {1989}}

@article{Bankier2002,
	Author = {Alexander A Bankier and Afarine Madani and Pierre Alain Gevenois},
	Journal = {Crit Rev Comput Tomogr},
	Number = {6},
	Pages = {399--417},
	Timestamp = {2009.05.18},
	Title = {{CT} quantification of pulmonary emphysema: assessment of lung structure and function.},
	Volume = {43},
	Year = {2002}}

@article{Bankier1999,
	Author = {A. A. Bankier and V. De Maertelaer and C. Keyzer and P. A. Gevenois},
	Journal = {Radiology},
	Month = {Jun},
	Number = {3},
	Pages = {851--858},
	Timestamp = {2009.05.18},
	Title = {Pulmonary emphysema: subjective visual grading versus objective quantification with macroscopic morphometry and thin-section {CT} densitometry.},
	Volume = {211},
	Year = {1999}}

@article{Bao2004,
	Author = {Yufang Bao and Hamid Krim},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {1},
	Owner = {tustison},
	Pages = {63-72},
	Title = {Smart Nonlinear Diffusion: A Probabilistic Approach},
	Volume = {26},
	Year = {2004}}

@article{Barone1992,
	Author = {Piero Barone and Giovanni Sebastiani},
	Journal = {IEEE Transactions on Medical Imaging},
	Number = {2},
	Owner = {tustison},
	Pages = {250-259},
	Title = {A New Method of Magnetic Resonance Image Reconstruction with Short Acquisition Time and Truncation Artifact Reduction},
	Volume = {11},
	Year = {1992}}

@article{Barrett1997,
	Author = {W. A. Barrett and E. N. Mortensen},
	Journal = {Medical Image Analysis},
	Month = {September},
	Number = {4},
	Pages = {331-341},
	Timestamp = {2008.05.21},
	Title = {Interactive Live-Wire Boundary Extraction},
	Volume = {1},
	Year = {1997}}

@inproceedings{Barrett1996,
	Author = {W. A. Barrett and E. N. Mortensen},
	Booktitle = {Visualization in Biomedical Computing},
	Pages = {183-192},
	Timestamp = {2008.05.21},
	Title = {Fast, accurate and reproducible live-wire boundary extraction},
	Year = {1996}}

@article{Barron1998,
	Author = {Andrew Barron and Jorma Rissanen and Bin Yu},
	Journal = {IEEE Transactions on Information Theory},
	Number = {6},
	Owner = {tustison},
	Pages = {2743-2760},
	Title = {The Minimum Description Length Principle in Coding and Modeling},
	Volume = {44},
	Year = {1998}}

@article{Barsky1983,
	Author = {Brian A. Barsky and John C. Beatty},
	Journal = {ACM Transactions on Graphics},
	Number = {2},
	Owner = {tustison},
	Pages = {109-134},
	Title = {Local Control of Bias and Tension in Beta-splines},
	Volume = {2},
	Year = {1983}}

@inproceedings{Barthe1998,
	Author = {L. Barthe and V. Gaildrat and R. Caubet},
	Booktitle = {CSG '98 Proceedings},
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	Owner = {tustison},
	Pages = {17-31},
	Title = {Combining implicit surfaces with soft blending in a CSG tree},
	Year = {1998}}

@article{Bartoli2008,
	Author = {Bartoli, Adrien},
	Doi = {10.1109/TPAMI.2008.22},
	Journal = IEEE_J_PAMI,
	Month = {Dec.},
	Number = {12},
	Pages = {2098--2108},
	Timestamp = {2008.11.26},
	Title = {Groupwise Geometric and Photometric Direct Image Registration},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2008.22}}

@inproceedings{Bascle1993,
	Author = {B. Bascle and R. Deriche},
	Booktitle = {4th International Conference on Computer Vision},
	Owner = {tustison},
	Title = {Stereo Matching, Reconstruction and Refinement of 3D Curves Using Deformable Contours},
	Year = {1993}}

@article{Basu1998,
	Author = {A. Basu and I. Harris and N. Hjort and M. Jones},
	Journal = {Biometrika},
	Pages = {549-559},
	Timestamp = {2008.09.06},
	Title = {Robust and efficient estimation by minimizing a density power divergence},
	Volume = {85},
	Year = {1998}}

@article{Becker1998,
	Author = {M. D. Becker and Y. M. Berkmen and J. H. Austin and I. K. Mun and B. M. Romney and A. Rozenshtein and P. A. Jellen and C. K. Yip and B. Thomashow and M. E. Ginsburg},
	Journal = {Am J Respir Crit Care Med},
	Month = {May},
	Number = {5 Pt 1},
	Pages = {1593--1599},
	Timestamp = {2009.05.18},
	Title = {Lung volumes before and after lung volume reduction surgery: quantitative {CT} analysis.},
	Volume = {157},
	Year = {1998}}

@article{Beg2005,
	Address = {Hingham, MA, USA},
	Author = {M. F. Beg and M. I. Miller and A. Trouv\'{e} and L. Younes},
	Doi = {http://dx.doi.org/10.1023/B:VISI.0000043755.93987.aa},
	Issn = {0920-5691},
	Journal = {Int. J. Comput. Vision},
	Number = {2},
	Pages = {139--157},
	Publisher = {Kluwer Academic Publishers},
	Title = {Computing Large Deformation Metric Mappings via Geodesic Flows of Diffeomorphisms},
	Volume = {61},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1023/B:VISI.0000043755.93987.aa}}

@book{Berg2000,
	Author = {M. de Berg and M. van Kreveld and M. Overmars and O. Scharzkopf},
	Publisher = {Springer},
	Timestamp = {2007.12.11},
	Title = {Computational Geometry: Algorithms and Applications},
	Year = {2000}}

@article{Berger2003,
	Author = {Patrick Berger and Francois Laurent and Hugues Begueret and Vincent Perot and Rozen Rouiller and Chantal Raherison and Mathieu Molimard and Roger Marthan and J. Manuel Tunon-de-Lara},
	Journal = {Radiology},
	Month = {Jul},
	Number = {1},
	Pages = {85--94},
	Timestamp = {2009.05.18},
	Title = {Structure and function of small airways in smokers: relationship between air trapping at {CT} and airway inflammation.},
	Volume = {228},
	Year = {2003}}

@article{Bergholm1987,
	Author = {Fredrik Bergholm},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {6},
	Owner = {tustison},
	Pages = {726-741},
	Title = {Edge Focusing},
	Volume = {9},
	Year = {1987}}

@article{Besag1986,
	Author = {Julian Besag},
	Journal = {J. R. Statist. Soc. B},
	Number = {3},
	Owner = {tustison},
	Pages = {259-302},
	Title = {On the Statistical Analysis of Dirty PIctures},
	Volume = {48},
	Year = {1986}}

@article{Besl1992,
	Author = {Paul J. Besl and Neil D. McKay},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {2},
	Owner = {tustison},
	Pages = {239-256},
	Title = {A Method for Registration of 3-{D} Shapes},
	Volume = {14},
	Year = {1992}}

@article{Bey2002,
	Author = {M. J. Bey and H. K. Song and F. W. Wehrli and L. J. Soslowsky},
	Journal = {Journal of Biomechanical Engineering},
	Pages = {253-261},
	Timestamp = {2007.03.15},
	Title = {A Noncontact, Nondestructive Method for Quantifying Intratissue Deformations and Strains},
	Volume = {124},
	Year = {2002}}

@article{Bishnu2007,
	Author = {Bishnu, A. and Bhattacharya, B.B.},
	Doi = {10.1109/TPAMI.2007.43},
	Journal = IEEE_J_PAMI,
	Month = {Feb.},
	Number = {2},
	Pages = {350--355},
	Timestamp = {2008.11.26},
	Title = {Stacked Euler Vector (SERVE): A Gray-Tone Image Feature Based on Bit-Plane Augmentation},
	Volume = {29},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.43}}

@article{Blake1998,
	Author = {A. Blake and B. Bascle and M. Isard and J. MacCormick},
	Journal = {Philosophical Transactions of the Royal Society of London A},
	Number = {356},
	Owner = {tustison},
	Pages = {1283-1302},
	Title = {Statistical models of visual shape and motion},
	Year = {1998}}

@article{Blake1993,
	Author = {Andrew Blake and Rupert Curwen and Andrew Zisserman},
	Journal = {International Journal of Computer Vision},
	Number = {2},
	Owner = {tustison},
	Pages = {127-145},
	Title = {A Framework for Spatiotemporal Control in the Tracking of Visual Contours},
	Volume = {11},
	Year = {1993}}

@article{Blake1995,
	Author = {Andrew Blake and Michael Isard and David Reynard},
	Journal = {Artifical Intelligence},
	Number = {78},
	Owner = {tustison},
	Pages = {179-212},
	Title = {Learning to track the visual motion of contours},
	Year = {1995}}

@inproceedings{Blake1994,
	Author = {Andrew Blake and Michael Isard and David Reynard},
	Booktitle = {Proc. IEEE International Conference on Decision Theory and Control},
	Owner = {tustison},
	Pages = {3788-3793},
	Year = {1994}}

@article{Boedeker2004,
	Author = {Kirsten L Boedeker and Michael F McNitt-Gray and Sarah R Rogers and Dao A Truong and Matthew S Brown and David W Gjertson and Jonathan G Goldin},
	Journal = {Radiology},
	Month = {Jul},
	Number = {1},
	Pages = {295--301},
	Timestamp = {2009.05.18},
	Title = {Emphysema: effect of reconstruction algorithm on {CT} imaging measures.},
	Volume = {232},
	Year = {2004}}

@article{Bookstein1989,
	Author = {F. L. Bookstein},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {6},
	Pages = {567-585},
	Timestamp = {2007.10.22},
	Title = {Principal Warps: Thin-plate splines and the decomposition of deformations},
	Volume = {11},
	Year = {1989}}

@inbook{Boor1993,
	Author = {Carl de Boor},
	Chapter = {B-spline basics},
	Editor = {Les Piegl},
	Owner = {tustison},
	Pages = {27-49},
	Publisher = {American Press, San Diego, CA},
	Title = {Fundamental Developments of Computer-Aided Geometric Modeling},
	Year = {1993}}

@article{Boor1972a,
	Author = {C. de Boor},
	Journal = {Jour. Approx. Theory},
	Pages = {50-62},
	Timestamp = {2006.12.20},
	Title = {On calculating with {B}-splines},
	Volume = {6},
	Year = {1972}}

@article{Borenstein2008,
	Author = {Borenstein, Eran and Ullman, Shimon},
	Doi = {10.1109/TPAMI.2007.70840},
	Journal = IEEE_J_PAMI,
	Month = {Dec.},
	Number = {12},
	Pages = {2109--2125},
	Timestamp = {2008.11.26},
	Title = {Combined Top-Down/Bottom-Up Segmentation},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70840}}

@article{Bousquet2000,
	Author = {J. Bousquet and P. K. Jeffery and W. W. Busse and M. Johnson and A. M. Vignola},
	Journal = {Am J Respir Crit Care Med},
	Keywords = {Animals; Asthma; Bronchi; Bronchoconstriction; Humans; Inflammation},
	Month = {May},
	Number = {5},
	Pages = {1720--1745},
	Pmid = {10806180},
	Timestamp = {2007.09.08},
	Title = {Asthma. From bronchoconstriction to airways inflammation and remodeling.},
	Volume = {161},
	Year = {2000}}

@inproceedings{Boykov2000,
	Author = {Yuri Boykov and Marie-Pierre Jolly},
	Booktitle = {Proceedings of MICCAI},
	Owner = {tustison},
	Pages = {276-286},
	Title = {Interactive Organ Segmentation Using Graph Cuts},
	Year = {2000}}

@article{Boykov2004,
	Abstract = {After [15], [31], [19], [8], [25], [5], minimum cut/maximum flow algorithms on graphs emerged as an increasingly useful tool for exact or approximate energy minimization in low-level vision. The combinatorial optimization literature provides many min-cut/max-flow algorithms with different polynomial time complexity. Their practical efficiency, however, has to date been studied mainly outside the scope of computer vision. The goal of this paper is to provide an experimental comparison of the efficiency of min-cut/max flow algorithms for applications in vision. We compare the running times of several standard algorithms, as well as a new algorithm that we have recently developed. The algorithms we study include both Goldberg-Tarjan style "push-relabel" methods and algorithms based on Ford-Fulkerson style "augmenting paths." We benchmark these algorithms on a number of typical graphs in the contexts of image restoration, stereo, and segmentation. In many cases, our new algorithm works several times faster than any of the other methods, making near real-time performance possible. An implementation of our max-flow/min-cut algorithm is available upon request for research purposes.},
	Author = {Yuri Boykov and Vladimir Kolmogorov},
	Journal = {IEEE Trans Pattern Anal Mach Intell},
	Keywords = {Algorithms, Artificial Intelligence, Cluster Analysis, Energy Transfer, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Information Storage and Retrieval, Pattern Recognition, Automated, Photogrammetry, Photography, Reproducibility of Results, Sensitivity and Specificity, 15742889},
	Month = {Sep},
	Number = {9},
	Owner = {tustison},
	Pages = {1124-37},
	Title = {An experimental comparison of min-cut/max-flow algorithms for energy minimization in vision.},
	Volume = {26},
	Year = {2004}}

@inproceedings{Boykov2003,
	Author = {Yuri Boykov and Vladimir Kolmogorov},
	Booktitle = {Proceedings of the International Conference on Computer Vision},
	Owner = {tustison},
	Title = {Computing Geodesics and Minimal Surfaces via Graph Cuts},
	Year = {2003}}

@article{Boykov2001,
	Author = {Yuri Boykov and Olga Veksler and Ramin Zabih},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {11},
	Owner = {tustison},
	Pages = {1222-1239},
	Title = {Fast Approximate Energy Minimization via Graph Cuts},
	Volume = {23},
	Year = {2001}}

@inproceedings{Boykov2001a,
	Author = {Yuri Y. Boykov and Marie-Pierre Jolly},
	Booktitle = {Proceedings of the International Conference on Computer Vision},
	Owner = {tustison},
	Pages = {105-112},
	Title = {Interactive Graph Cuts for Optimal Boundary and Region Segmentation of Objects in N-D Images},
	Volume = {1},
	Year = {2001}}

@article{Breckon2008,
	Author = {Breckon, Toby P. and Fisher, Robert B.},
	Doi = {10.1109/TPAMI.2008.153},
	Journal = IEEE_J_PAMI,
	Month = {Dec.},
	Number = {12},
	Pages = {2249--2255},
	Timestamp = {2008.11.26},
	Title = {Three-Dimensional Surface Relief Completion Via Nonparametric Techniques},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2008.153}}

@article{Bredno2003,
	Author = {Bredno, J. and Lehmann, T.M. and Spitzer, K.},
	Doi = {10.1109/TPAMI.2003.1195990},
	Journal = IEEE_J_PAMI,
	Month = {May},
	Number = {5},
	Pages = {550--563},
	Timestamp = {2008.11.26},
	Title = {A general discrete contour model in two, three, and four dimensions for topology-adaptive multichannel segmentation},
	Volume = {25},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2003.1195990}}

@article{Breu1995,
	Author = {Heinz Breu and Joseph Gil and David Kirkpatrick and Michael Werman},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {5},
	Owner = {tustison},
	Pages = {529-533},
	Title = {Linear Time Euclidean Distance Transform Algorithms},
	Volume = {17},
	Year = {1995}}

@article{Brown1992,
	Author = {Lisa Gottsfield Brown},
	Journal = {ACM Computing Surveys},
	Month = {December},
	Number = {4},
	Owner = {tustison},
	Pages = {325-376},
	Title = {A Survey of Image Registration Techniques},
	Volume = {24},
	Year = {1992}}

@article{Brown2000,
	Author = {M. S. Brown and J. G. Goldin and M. F. McNitt-Gray and L. E. Greaser and A. Sapra and K. T. Li and J. W. Sayre and K. Martin and D. R. Aberle},
	Journal = {Med Phys},
	Month = {Mar},
	Number = {3},
	Pages = {592--598},
	Timestamp = {2009.05.18},
	Title = {Knowledge-based segmentation of thoracic computed tomography images for assessment of split lung function.},
	Volume = {27},
	Year = {2000}}

@article{Brown2005,
	Author = {Matthew S Brown and Sumit K Shah and Richard C Pais and Yeng-Zhong Lee and Michael F McNitt-Gray and Jonathan G Goldin and Alfonso F Cardenas and Denise R Aberle},
	Journal = {IEEE Trans Inf Technol Biomed},
	Month = {Mar},
	Number = {1},
	Pages = {99--108},
	Timestamp = {2009.05.18},
	Title = {Database design and implementation for quantitative image analysis research.},
	Volume = {9},
	Year = {2005}}

@article{Bunke2004,
	Author = {Bunke, H. and Bengio, S. and Vinciarelli, A.},
	Doi = {10.1109/TPAMI.2004.14},
	Journal = IEEE_J_PAMI,
	Month = {June},
	Number = {6},
	Pages = {709--720},
	Timestamp = {2008.11.26},
	Title = {Offline recognition of unconstrained handwritten texts using HMMs and statistical language models},
	Volume = {26},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2004.14}}

@article{Burbea1982,
	Author = {J. Burbea and C. R. Rao},
	Journal = {IEEE Transactions on Information Theory},
	Pages = {489-495},
	Timestamp = {2008.08.14},
	Title = {On the convexity of some divergence measures on entropy functions},
	Volume = {28},
	Year = {1982}}

@article{Cai2007a,
	Abstract = {A new technique is demonstrated in six healthy human subjects that combines grid-tagging and hyperpolarized helium-3 MRI to assess regional lung biomechanical function and quantitative ventilation. 2D grid-tagging, achieved by applying sinc-modulated RF-pulse trains along the frequency- and phase-encoding directions, was followed by a multislice fast low-angle shot (FLASH)-based acquisition at inspiration and expiration. The displacement vectors, first and second principal strains, and quantitative ventilation were computed, and mean values were calculated for the upper, middle, and lower lung regions. Displacements in the lower region were significantly greater than those in either the middle or upper region (P < 0.005), while there were no significant differences between the three regions for the two principal strains and quantitative ventilation (P = 0.11-0.92). Variations in principal strains and ventilation were greater between subjects than between lung zones within individual subjects. This technique has the potential to provide insight into regional biomechanical alterations of lung function in a variety of lung diseases.},
	Author = {J. Cai and T. A. Altes and G. W. Miller and K. Sheng and P. W. Read and J. F. Mata and X. Zhong and G. D. Cates and E. E. de Lange and J. P. Mugler and J. R. Brookeman},
	Doi = {10.1002/mrm.21288},
	Journal = {Magn Reson Med},
	Month = {Aug},
	Number = {2},
	Pages = {373--380},
	Pmid = {17654579},
	Timestamp = {2007.09.09},
	Title = {MR grid-tagging using hyperpolarized helium-3 for regional quantitative assessment of pulmonary biomechanics and ventilation.},
	Url = {http://dx.doi.org/10.1002/mrm.21288},
	Volume = {58},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/mrm.21288}}

@inproceedings{Cai2006,
	Author = {J. Cai and T. A. Altes and W. Miller and J. F. Mata and X. Zhong and E. E. de Lange and J. P. Mugler III and J. R. Brookeman},
	Booktitle = {Proceedings of ISMRM},
	Timestamp = {2006.12.20},
	Title = {{MR} Grid-Tagging Using Hyperpolarized Helium-3 for Quantitative Assessment of Regional Pulmonary Biomechanics},
	Year = {2006}}

@article{Cai2007,
	Abstract = {Purpose: To measure lung motion between end-inhalation and end-exhalation using a hyperpolarized helium-3 (HP (3)He) magnetic resonance (MR) tagging technique. Methods and Materials: Three healthy volunteers underwent MR tagging studies after inhalation of 1 L HP (3)He gas diluted with nitrogen. Multiple-slice two-dimensional and volumetric three-dimensional MR tagged images of the lungs were obtained at end-inhalation and end-exhalation, and displacement vector maps were computed. Results: The grids of tag lines in the HP (3)He MR images were well defined at end-inhalation and remained evident at end-exhalation. Displacement vector maps clearly demonstrated the regional lung motion and deformation that occurred during exhalation. Discontinuity and differences in motion pattern between two adjacent lung lobes were readily resolved. Conclusions: Hyperpolarized helium-3 MR tagging technique can be used for direct in vivo measurement of respiratory lung motion on a regional basis. This technique may lend new insights into the regional pulmonary biomechanics and thus provide valuable information for the deformable registration of lung.},
	Author = {Jing Cai and G. Wilson Miller and Talissa A Altes and Paul W Read and Stanley H Benedict and Eduard E de Lange and Gordon D Cates and James R Brookeman and John P Mugler and Ke Sheng},
	Doi = {10.1016/j.ijrobp.2007.02.011},
	Journal = {Int J Radiat Oncol Biol Phys},
	Month = {Jul},
	Number = {3},
	Pages = {650--653},
	Pii = {S0360-3016(07)00314-8},
	Pmid = {17445997},
	Timestamp = {2007.06.06},
	Title = {Direct Measurement of Lung Motion Using Hyperpolarized Helium-3 MR Tagging.},
	Url = {http://dx.doi.org/10.1016/j.ijrobp.2007.02.011},
	Volume = {68},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.ijrobp.2007.02.011}}

@article{Cai2007b,
	Author = {Jing Cai and G. Wilson Miller and T. A. Altes and P. W. Read and S. H. Benedict and E. E. de Lange and G. D. Cates and J. R. Brookeman and J. P. Mugler and K. Sheng},
	Journal = {Int. J. Radiation Oncology Biol. Phys.},
	Number = {3},
	Pages = {650-653},
	Timestamp = {2007.09.09},
	Title = {Direct Measurement of Lung Motion Using Hyperpolarized Helium-3 MR Tagging},
	Volume = {68},
	Year = {2007}}

@article{Chandrashekara2004,
	Abstract = {Tagged magnetic resonance imaging (MRI) is unique in its ability to noninvasively image the motion and deformation of the heart in vivo, but one of the fundamental reasons limiting its use in the clinical environment is the absence of automated tools to derive clinically useful information from tagged MR images. In this paper, we present a novel and fully automated technique based on nonrigid image registration using multilevel free-form deformations (MFFDs) for the analysis of myocardial motion using tagged MRI. The novel aspect of our technique is its integrated nature for tag localization and deformation field reconstruction using image registration and voxel based similarity measures. To extract the motion field within the myocardium during systole we register a sequence of images taken during systole to a set of reference images taken at end-diastole, maximizing the normalized mutual information between the images. We use both short-axis and long-axis images of the heart to estimate the full four-dimensional motion field within the myocardium. We also present validation results from data acquired from twelve volunteers.},
	Author = {Raghavendra Chandrashekara and Raad H Mohiaddin and Daniel Rueckert},
	Institution = {Visual Information Processing Group, Department of Computing, Imperial College, 180 Queen's Gate, London SW7 2AZ, U.K. rc3@doc.ic.ac.uk},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Algorithms; Cluster Analysis; Computer Simulation; Heart Ventricles; Humans; Image Enhancement; Image Interpretation, Computer-Assisted; Imaging, Three-Dimensional; Information Storage and Retrieval; Magnetic Resonance Imaging; Movement; Pattern Recognition, Automated; Reproducibility of Results; Sensitivity and Specificity; Signal Processing, Computer-Assisted; Subtraction Technique},
	Month = {Oct},
	Number = {10},
	Pages = {1245--1250},
	Pmid = {15493692},
	Timestamp = {2008.01.12},
	Title = {Analysis of 3-D myocardial motion in tagged MR images using nonrigid image registration.},
	Volume = {23},
	Year = {2004}}

@article{Charalampidis2005,
	Author = {Charalampidis, D.},
	Doi = {10.1109/TPAMI.2005.230},
	Journal = IEEE_J_PAMI,
	Month = {Dec.},
	Number = {12},
	Pages = {1856--1865},
	Timestamp = {2008.11.26},
	Title = {A modified k-means algorithm for circular invariant clustering},
	Volume = {27},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2005.230}}

@article{Chen1989,
	Author = {Chen, C.-C. and DaPonte, J.S. and Fox, M.D.},
	Doi = {10.1109/42.24861},
	Issn = {0278-0062},
	Journal = {IEEE Transactions on Medical Imaging},
	Keywords = {Brownian motion, fractals, patient diagnosis, edge detection, edge enhancement, fractal feature analysis, fractal feature classification, fractional Brownian motion, linear intensity transformation, medical imaging, statistical characteristics},
	Number = {2},
	Pages = {133-142},
	Timestamp = {2009.02.07},
	Title = {Fractal feature analysis and classification in medical imaging},
	Volume = {8},
	Year = {1989},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/42.24861}}

@inproceedings{Chen2006,
	Author = {J. Chen and N. J. Tustison and A. A. Amini},
	Booktitle = {Proceedings of the SPIE: Medical Imaging},
	Timestamp = {2007.09.25},
	Title = {Accurate recovery of 4D left ventricular deformations using volumetric B-splines incorporating phase-based displacement estimates.},
	Year = {2006}}

@article{Chen2001,
	Abstract = {While MR imaging with tagged magnetization has shown great utility in the study of muscle mechanics, the evaluation of pulmonary mechanics has long been hindered by the technical difficulties in MR imaging of lung parenchyma. In this study, a fast MR grid-tagging technique is described for dynamic assessment of regional pulmonary deformation. The method is based on a fast FLASH sequence with short TR and short TE. Tagging was achieved by using double DANTE pulse train or inversion pulses. Our results show that this technique is able to detect changes of the tagging grid caused by physiological deformation of the lung. Quantitative analysis of the data shows that this method is capable of assessing local pulmonary mechanics. The application of this technique could improve our understanding of ventilatory control, and thus provide a unique metric for assessing pulmonary disorders. Magn Reson Med 45:24-28, 2001.},
	Author = {Q. Chen and V. M. Mai and A. A. Bankier and V. J. Napadow and R. J. Gilbert and R. R. Edelman},
	Journal = {Magn Reson Med},
	Keywords = {Adult; Female; Humans; Lung; Magnetic Resonance Imaging; Male; Middle Aged; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, P.H.S.; Respiratory Mechanics},
	Month = {Jan},
	Number = {1},
	Pages = {24--28},
	Pii = {3.0.CO;2-6},
	Pmid = {11146481},
	Timestamp = {2006.12.20},
	Title = {Ultrafast {MR} grid-tagging sequence for assessment of local mechanical properties of the lungs.},
	Volume = {45},
	Year = {2001}}

@article{Christensen2003,
	Author = {Gary E. Christensen and Hans J. Johnson},
	Journal = {Journal of Electronic Imaging},
	Number = {1},
	Owner = {tustison},
	Pages = {106-117},
	Title = {Invertibility and Transitivity analysis for nonrigid image registration},
	Volume = {12},
	Year = {2003}}

@article{Christensen2001,
	Author = {G. E. Christensen and H. J. Johnson},
	Journal = {IEEE Transactions on Medical Imaging},
	Number = {7},
	Owner = {tustison},
	Pages = {568-582},
	Title = {Consistent Image Registration},
	Volume = {20},
	Year = {2001}}

@article{Christensen1996,
	Author = {Gary E. Christensen and Richard D. Rabbitt and Michael I. Miller},
	Journal = {IEEE Transactions on Image Processing},
	Number = {10},
	Owner = {tustison},
	Pages = {1435-1447},
	Title = {Deformable Templates Using Large Deformation Kinematics},
	Volume = {5},
	Year = {1996}}

@article{Christensen96,
	Author = {Gary E. Christensen and Richard D. Rabbitt and Michael I. Miller},
	Journal = {IEEE Transactions on Image Processing},
	Number = {10},
	Pages = {1435-1447},
	Title = {Deformable templates using large deformation kinematics},
	Volume = {5},
	Year = {1996}}

@article{Chu1990,
	Author = {A. Chu and C. M. Sehgal and J. F. Greenleaf},
	Journal = {Pattern Recognition Letters},
	Pages = {415-420},
	Timestamp = {2008.05.26},
	Title = {Use of gray value distribution of run lengths for texture analysis},
	Volume = {11},
	Year = {1990}}

@article{Chui2003,
	Author = {Haili Chui and Anand Rangarajan},
	Journal = {Computer Vision and Image Understanding},
	Pages = {114-141},
	Timestamp = {2007.10.23},
	Title = {A new point matching algorithm for non-rigid registration},
	Volume = {89},
	Year = {2003}}

@article{Cline1976,
	Author = {R. E. Cline and R. J. Plemmons},
	Journal = {SIAM Review},
	Number = {1},
	Owner = {tustison},
	Pages = {92-106},
	Title = {L2-Solutions to Underdetermined Linear Systems},
	Volume = {18},
	Year = {1976}}

@article{Cluzel2000,
	Abstract = {Magnetic resonance (MR) imaging of the thorax with three-dimensional (3D) reconstruction and functional quantification was evaluated as a tool for structure-function evaluation of chest-wall mechanics. Good agreement was found between the corresponding spirometric and MR imaging values of lung volumes. Fast MR imaging of the thorax with 3D reconstruction should improve the ability to evaluate the inspiratory pump in clinical and research investigations.},
	Author = {P. Cluzel and T. Similowski and C. Chartrand-Lefebvre and M. Zelter and J. P. Derenne and P. A. Grenier},
	Journal = {Radiology},
	Keywords = {Adult; Algorithms; Diaphragm; Feasibility Studies; Functional Residual Capacity; Humans; Image Processing, Computer-Assisted; Inhalation; Lung; Lung Volume Measurements; Magnetic Resonance Imaging; Male; Phantoms, Imaging; Pressure; Reproducibility of Results; Residual Volume; Respiratory Mechanics; Ribs; Spirometry; Thorax; Total Lung Capacity},
	Month = {May},
	Number = {2},
	Pages = {574--583},
	Pmid = {10796942},
	Timestamp = {2008.01.24},
	Title = {Diaphragm and chest wall: assessment of the inspiratory pump with MR imaging-preliminary observations.},
	Volume = {215},
	Year = {2000}}

@article{Cocosco2003,
	Abstract = {A novel, fully automatic, adaptive, robust procedure for brain tissue classification from 3D magnetic resonance head images (MRI) is described in this paper. The procedure is adaptive in that it customizes a training set, by using a 'pruning' strategy, such that the classification is robust against anatomical variability and pathology. Starting from a set of samples generated from prior tissue probability maps (a 'model') in a standard, brain-based coordinate system ('stereotaxic space'), the method first reduces the fraction of incorrectly labeled samples in this set by using a minimum spanning tree graph-theoretic approach. Then, the corrected set of samples is used by a supervised kNN classifier for classifying the entire 3D image. The classification procedure is robust against variability in the image quality through a non-parametric implementation: no assumptions are made about the tissue intensity distributions. The performance of this brain tissue classification procedure is demonstrated through quantitative and qualitative validation experiments on both simulated MRI data (10 subjects) and real MRI data (43 subjects). A significant improvement in output quality was observed on subjects who exhibit morphological deviations from the model due to aging and pathology.},
	Author = {Chris A Cocosco and Alex P Zijdenbos and Alan C Evans},
	Journal = {Med Image Anal},
	Keywords = {Adult, Aged, Automation, Brain, Female, Humans, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Magnetic Resonance Imaging, Male, Middle Aged, Models, Anatomic, Phantoms, Imaging, 14561555},
	Month = {Dec},
	Number = {4},
	Owner = {tustison},
	Pages = {513-27},
	Pii = {S1361841503000379},
	Title = {A fully automatic and robust brain {MRI} tissue classification method.},
	Volume = {7},
	Year = {2003}}

@book{Cohen1988,
	Author = {J. Cohen},
	Publisher = {Erlbaum},
	Timestamp = {2008.01.14},
	Title = {Statistical power analysis for the behavioral sciences},
	Year = {1988}}

@article{Cook2007,
	Journal = {Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv},
	Number = {Pt 1},
	Pages = {817--824},
	Timestamp = {2009.05.18},
	Title = {How do registration parameters affect quantitation of lung kinematics?},
	Volume = {10},
	Year = {2007}}

@article{Coquillart1990,
	Author = {Sabine Coquillart},
	Journal = {Computer Graphics},
	Number = {4},
	Owner = {tustison},
	Pages = {187-196},
	Title = {Extended Free-Form Deformation: A Sculpturing Tool for 3D Geometric Modeling},
	Volume = {24},
	Year = {1990}}

@article{Cordero2004,
	Author = {Raul R. Cordero and Pedro Roth},
	Journal = {Measurement Science Technology},
	Owner = {tustison},
	Pages = {1885-1891},
	Title = {Whole-field strain uncertainty evaluation by a Monte Carlo method},
	Volume = {15},
	Year = {2004}}

@article{Costantini2004,
	Author = {Alessandro Maria Costantini and Giuseppina Sallustio and Teresa Misciasci and Giuseppe Maria Corbo and Salvatore Valente and Tommaso Pirronti and Pasquale Marano},
	Journal = {Radiol Med (Torino)},
	Number = {1-2},
	Pages = {17--27},
	Timestamp = {2009.05.18},
	Title = {{CT} and functional respiratory tests. Evaluation of efficacy of bronchodilator therapy in chronic obstructive pulmonary disease (COPD).},
	Volume = {108},
	Year = {2004}}

@inproceedings{Cour,
	Author = {Timothee Cour and Florence Benezit and Jianbo Shi},
	Owner = {tustison},
	Title = {Spectral Segmentation with Multiscale Graph Decomposition}}

@article{Cox1972,
	Author = {M. G. Cox},
	Journal = {Jour. Inst. Math. Applic.},
	Pages = {134-149},
	Timestamp = {2006.04.12},
	Title = {The numerical evaluation of B-splines},
	Volume = {10},
	Year = {1972}}

@article{Cox1971,
	Author = {M. G. Cox},
	Journal = {J. Inst. Maths Applics},
	Owner = {tustison},
	Pages = {36-52},
	Title = {Curve Fitting with Piecewise Polynomials},
	Volume = {8},
	Year = {1971}}

@article{Coxson2007,
	Author = {H. O. Coxson},
	Journal = {Eur Respir J},
	Month = {Jun},
	Number = {6},
	Pages = {1075--1077},
	Timestamp = {2009.05.18},
	Title = {Computed tomography and monitoring of emphysema.},
	Volume = {29},
	Year = {2007}}

@article{Coxson2001,
	Author = {H. O. Coxson and J. C. Hogg},
	Journal = {Am J Respir Crit Care Med},
	Month = {May},
	Number = {6},
	Pages = {1500--1501},
	Timestamp = {2009.05.18},
	Title = {Erratum: a quantification of the lung surface area in emphysema using computed tomography.},
	Volume = {163},
	Year = {2001}}

@article{Coxson1995,
	Journal = {J Appl Physiol},
	Month = {Nov},
	Number = {5},
	Pages = {1525--1530},
	Timestamp = {2009.05.18},
	Title = {Measurement of lung expansion with computed tomography and comparison with quantitative histology.},
	Volume = {79},
	Year = {1995}}

@article{Coxson2005,
	Author = {Harvey O Coxson and Robert M Rogers},
	Journal = {Acad Radiol},
	Month = {Nov},
	Number = {11},
	Pages = {1457--1463},
	Timestamp = {2009.05.18},
	Title = {Quantitative computed tomography of chronic obstructive pulmonary disease.},
	Volume = {12},
	Year = {2005}}

@article{Coxson2005a,
	Author = {Harvey O Coxson and Robert M Rogers},
	Journal = {Semin Respir Crit Care Med},
	Month = {Apr},
	Number = {2},
	Pages = {211--220},
	Timestamp = {2009.05.18},
	Title = {New concepts in the radiological assessment of {COPD}.},
	Volume = {26},
	Year = {2005}}

@article{Coxson1999,
	Journal = {Am J Respir Crit Care Med},
	Month = {Mar},
	Number = {3},
	Pages = {851--856},
	Timestamp = {2009.05.18},
	Title = {A quantification of the lung surface area in emphysema using computed tomography.},
	Volume = {159},
	Year = {1999}}

@article{Crum2004,
	Author = {W. R. Crum and T. Hartkens and D. L. G. Hill},
	Journal = {The British Journal of Radiology},
	Owner = {tustison},
	Pages = {140-153},
	Title = {Non-rigid image registration: theory and practice},
	Volume = {77},
	Year = {2004}}

@article{Dahmen1992,
	Author = {Wolfgang Dahmen and Charles A. Micchelli and Hans-Peter Seidel},
	Journal = {Mathematics of Computation},
	Number = {199},
	Owner = {tustison},
	Pages = {97-115},
	Title = {Blossoming Begets B-Spline Bases Built Better By B-Patches},
	Volume = {59},
	Year = {1992}}

@article{Damon2005,
	Author = {James Damon},
	Journal = {International Journal of Computer Vision},
	Number = {1},
	Owner = {tustison},
	Pages = {45-64},
	Title = {Determining the Geometry of Boundaries of Objects from Medial Data},
	Volume = {63},
	Year = {2005}}

@article{Danielsson1980,
	Author = {P. -E. Danielsson},
	Journal = {Computer Vision, Graphics, and Image Processing},
	Owner = {tustison},
	Pages = {227-248},
	Title = {Euclidean Distance Mapping},
	Volume = {14},
	Year = {1980}}

@article{Dasarathy1991,
	Author = {B. R. Dasarathy and E. B. Holder},
	Journal = {Pattern Recognition Letters},
	Pages = {497-502},
	Timestamp = {2008.05.26},
	Title = {Image characterizations based on joint gray-level run-length distributions},
	Volume = {12},
	Year = {1991}}

@article{Davatzikos1997,
	Author = {Christos Davatzikos},
	Journal = {Computer Vision and Image Understanding},
	Number = {2},
	Pages = {207-222},
	Timestamp = {2006.07.07},
	Title = {Spatial Transformation and Registration of Braim Images Using Elastically Deformable Models},
	Volume = {66},
	Year = {1997}}

@article{Davatzikos2003,
	Author = {Christos Davatzikos and Xiaodong Tao and Dinggang Shen},
	Journal = {IEEE Transactions on Medical Imaging},
	Number = {3},
	Owner = {tustison},
	Pages = {414-423},
	Title = {Hierarchical Active Shape Models, Using the Wavelet Transform},
	Volume = {22},
	Year = {2003}}

@article{Davis1997,
	Abstract = {Many image matching schemes are based on mapping coordinate locations, such as the locations of landmarks, in one image to corresponding locations in a second image. A new approach to this mapping (coordinate transformation), called the elastic body spline (EBS), is described. The spline is based on a physical model of a homogeneous, isotropic three-dimensional (3-D) elastic body. The model can approximate the way that some physical objects deform. The EBS as well as the affine transformation, the thin plate spline [1], [2] and the volume spline [3] are used to match 3-D magnetic resonance images (MRI's) of the breast that are used in the diagnosis and evaluation of breast cancer. These coordinate transformations are evaluated with different types of deformations and different numbers of corresponding (paired) coordinate locations. In all but one of the cases considered, using the EBS yields more similar images than the other methods.},
	Author = {MH Davis and A Khotanzad and DP Flamig and SE Harms},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Brain, Breast, Breast Neoplasms, Computer Graphics, Female, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Male, Phantoms, Imaging, 9184894},
	Month = {Jun},
	Number = {3},
	Owner = {tustison},
	Pages = {317-28},
	Title = {A physics-based coordinate transformation for 3-{D} image matching.},
	Volume = {16},
	Year = {1997}}

@article{Declerck2000,
	Abstract = {Through recent development of MR techniques, it is now possible to assess regional myocardial wall function in a non-invasive way. Using MR tagging, space is marked with planes which deform with the tissue, providing markers for tracking the local motion of the myocardium. Numerous methods to reconstruct the three-dimensional displacement field have been developed. The aim of this article is to provide a framework to quantitatively compare the performance of four methods the authors have developed. Five sets of experiments are described, and their results are reported. Instructions are also provided to perform similar tests on any method using the same data. The experiments show that some characteristic properties of the methods, such as sensitivity to noise or spatial resolution, can be quantitatively classified. Cross-comparison of performances show what range values for these properties can be considered acceptable.},
	Journal = {Phys Med Biol},
	Keywords = {Animals; Cardiac Pacing, Artificial; Cardiomyopathies; Dogs; Echocardiography; Elasticity; Heart Ventricles; Humans; Image Processing, Computer-Assisted; Models, Statistical; Myocardial Infarction; Reproducibility of Results; Ultrasonography},
	Month = {Jun},
	Number = {6},
	Pages = {1611--1632},
	Pmid = {10870714},
	Timestamp = {2007.09.09},
	Title = {Left ventricular motion reconstruction from planar tagged MR images: a comparison.},
	Volume = {45},
	Year = {2000}}

@article{Declerck1998,
	Author = {J. Declerck and J. Feldmar and N. Ayache},
	Journal = {Medical Image Analysis},
	Number = {1},
	Pages = {197-213},
	Timestamp = {2007.09.09},
	Title = {Definition of a 4D continuous planispheric transformation for the tracking and the analysis of LV motion},
	Volume = {4},
	Year = {1998}}

@article{Denney1995,
	Author = {T. Denney and J. Prince},
	Journal = {IEEE Transactions on Medical Imaging},
	Number = {4},
	Pages = {625-635},
	Timestamp = {2007.09.09},
	Title = {Reconstruction of 3D left ventricular motion from planar tagged cardiac MR images: An estimation-theoretic approach},
	Volume = {14},
	Year = {1995}}

@article{Denton1999,
	Abstract = {PURPOSE: A new nonrigid registration method, designed to reduce the effect of movement artifact in subtraction images from breast MR, is compared with existing rigid and affine registration methods. METHOD: Nonrigid registration was compared with rigid and affine registration methods and unregistered images using 54 gadolinium-enhanced 3D breast MR data sets. Twenty-seven data sets had been previously reported normal, and 27 contained a histologically proven carcinoma. The comparison was based on visual assessment and ranking by two radiologists. RESULTS: When analyzed by two radiologists independently, all three registration methods gave better-quality subtraction images than unregistered images (p < 0.01), but nonrigid registration gave significantly better results than the rigid and affine registration methods (p < 0.01). There was no significant difference between rigid and affine registration methods. CONCLUSION: Nonrigid registration significantly reduces the effects of movement artifact in subtracted contrast-enhanced breast MRI. This may enable better visualization of small tumors and those within a glandular breast.},
	Author = {ER Denton and LI Sonoda and D Rueckert and SC Rankin and C Hayes and MO Leach and DL Hill and DJ Hawkes},
	Journal = {J Comput Assist Tomogr},
	Keywords = {Adult, Aged, Algorithms, Breast, Comparative Study, Contrast Media, Female, Gadolinium DTPA, Humans, Magnetic Resonance Imaging, Middle Aged, Observer Variation, Research Support, Non-U.S. Gov't, Statistics, Nonparametric, 10524870},
	Number = {5},
	Owner = {tustison},
	Pages = {800-5},
	Title = {Comparison and evaluation of rigid, affine, and nonrigid registration of breast {MR} images.},
	Volume = {23},
	Year = {1999}}

@article{Diallo2000,
	Journal = {Chest},
	Month = {Dec},
	Number = {6},
	Pages = {1566--1575},
	Timestamp = {2009.05.18},
	Title = {Distribution of lung density and mass in patients with emphysema as assessed by quantitative analysis of {CT}.},
	Volume = {118},
	Year = {2000}}

@article{Dickinson2001,
	Author = {Sven Dickinson and Marcello Pelillo and Ramin Zabih},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {10},
	Owner = {tustison},
	Pages = {1049-1052},
	Title = {Introduction to the Special Section on Graph Algorithms in Computer Vision},
	Volume = {23},
	Year = {2001}}

@article{Ding2007,
	Author = {Xiaoqing Ding and Li Chen and Tao Wu},
	Doi = {10.1109/TPAMI.2007.26},
	Journal = IEEE_J_PAMI,
	Month = {Feb.},
	Number = {2},
	Pages = {195--204},
	Timestamp = {2008.11.26},
	Title = {Character Independent Font Recognition on a Single Chinese Character},
	Volume = {29},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.26}}

@article{Dirksen1999,
	Author = {A. Dirksen and J. H. Dijkman and F. Madsen and B. Stoel and D. C. Hutchison and C. S. Ulrik and L. T. Skovgaard and A. Kok-Jensen and A. Rudolphus and N. Seersholm and H. A. Vrooman and J. H. Reiber and N. C. Hansen and T. Heckscher and K. Viskum and J. Stolk},
	Journal = {Am J Respir Crit Care Med},
	Month = {Nov},
	Number = {5 Pt 1},
	Pages = {1468--1472},
	Timestamp = {2009.05.18},
	Title = {A randomized clinical trial of alpha(1)-antitrypsin augmentation therapy.},
	Volume = {160},
	Year = {1999}}

@article{Dong2005,
	Author = {Jian-xiong Dong and Krzyzak, A. and Suen, C.Y.},
	Doi = {10.1109/TPAMI.2005.77},
	Journal = IEEE_J_PAMI,
	Month = {April},
	Number = {4},
	Pages = {603--618},
	Timestamp = {2008.11.26},
	Title = {Fast SVM training algorithm with decomposition on very large data sets},
	Volume = {27},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2005.77}}

@article{Dougherty2006,
	Author = {Lawrence Dougherty and Drew A Torigian and John D Affusso and Jane C Asmuth and Warren B Gefter},
	Journal = {Acad Radiol},
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	Number = {1},
	Pages = {14--23},
	Timestamp = {2009.05.18},
	Title = {Use of an optical flow method for the analysis of serial {CT} lung images.},
	Volume = {13},
	Year = {2006}}

@article{Dupuis1998,
	Author = {P. Dupuis and U. Grenander and M. I. Miller},
	Text = {Dupuis P, Grenander U, Miller MI (1998) Variational problems on flows of diffeomorphisms for image matching. QUARTERLY OF APPLIED MATHEMATICS, 1998 SEP, V56 N3:587-600.},
	Title = {Variational problems on flows of diffeomorphisms for image matching},
	Url = {citeseer.comp.nus.edu.sg/67701.html},
	Year = {1998},
	Bdsk-Url-1 = {citeseer.comp.nus.edu.sg/67701.html}}

@article{Ebin1970,
	Author = {David G. Ebin and Jerrold Marsden},
	Journal = {Annals of Mathematics},
	Number = {92},
	Owner = {tustison},
	Pages = {102-163},
	Title = {Groups of diffeomorphisms and the motion of an incompressible fluid},
	Year = {1970}}

@article{Ederle2003,
	Author = {J. R. Ederle and C. P. Heussel and J. Hast and B. Fischer and E. J R Van Beek and S. Ley and M. Thelen and H. U. Kauczor},
	Journal = {Eur Radiol},
	Month = {Nov},
	Number = {11},
	Pages = {2454--2461},
	Timestamp = {2009.05.18},
	Title = {Evaluation of changes in central airway dimensions, lung area and mean lung density at paired inspiratory/expiratory high-resolution computed tomography.},
	Volume = {13},
	Year = {2003}}

@article{Endres2003,
	Author = {D. Endres and J. Schindelin},
	Journal = {IEEE Transactions on Information Theory},
	Pages = {1858-1860},
	Timestamp = {2008.09.05},
	Title = {A new metric for probability distributions},
	Volume = {49},
	Year = {2003}}

@article{Everitt2003,
	Author = {Everitt, R.A.J. and McOwan, P.W.},
	Doi = {10.1109/TPAMI.2003.1227991},
	Journal = IEEE_J_PAMI,
	Month = {Sept.},
	Number = {9},
	Pages = {1166--1172},
	Timestamp = {2008.11.26},
	Title = {Java-based Internet biometric authentication system},
	Volume = {25},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2003.1227991}}

@article{Fain2007,
	Abstract = {The noninvasive assessment of lung function using imaging is increasingly of interest for the study of lung diseases, including chronic obstructive pulmonary disease (COPD) and asthma. Hyperpolarized gas MRI (HP MRI) has demonstrated the ability to detect changes in ventilation, perfusion, and lung microstructure that appear to be associated with both normal lung development and disease progression. The physical characteristics of HP gases and their application to MRI are presented with an emphasis on current applications. Clinical investigations using HP MRI to study asthma, COPD, cystic fibrosis, pediatric chronic lung disease, and lung transplant are reviewed. Recent advances in polarization, pulse sequence development for imaging with Xe-129, and prototype low magnetic field systems dedicated to lung imaging are highlighted as areas of future development for this rapidly evolving technology.},
	Author = {Sean B Fain and Frank R Korosec and James H Holmes and Rafael O'Halloran and Ronald L Sorkness and Thomas M Grist},
	Doi = {10.1002/jmri.20876},
	Journal = {J Magn Reson Imaging},
	Month = {May},
	Number = {5},
	Pages = {910--923},
	Pmid = {17410561},
	Timestamp = {2007.06.06},
	Title = {Functional lung imaging using hyperpolarized gas MRI.},
	Url = {http://dx.doi.org/10.1002/jmri.20876},
	Volume = {25},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/jmri.20876}}

@article{Fang2008,
	Author = {Fang, Yi-Chin and Wu, Bo-Wen},
	Doi = {10.1109/TPAMI.2007.70839},
	Journal = IEEE_J_PAMI,
	Month = {Dec.},
	Number = {12},
	Pages = {2218--2228},
	Timestamp = {2008.11.26},
	Title = {Prediction of the Thermal Imaging Minimum Resolvable (Circle) Temperature Difference with Neural Network Application},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70839}}

@article{Faul2007,
	Abstract = {G*Power (Erdfelder, Faul, & Buchner, 1996) was designed as a general stand-alone power analysis program for statistical tests commonly used in social and behavioral research. G*Power 3 is a major extension of, and improvement over, the previous versions. It runs on widely used computer platforms (i.e., Windows XP, Windows Vista, and Mac OS X 10.4) and covers many different statistical tests of the t, F, and chi2 test families. In addition, it includes power analyses for z tests and some exact tests. G*Power 3 provides improved effect size calculators and graphic options, supports both distribution-based and design-based input modes, and offers all types of power analyses in which users might be interested. Like its predecessors, G*Power 3 is free.},
	Author = {Franz Faul and Edgar Erdfelder and Albert-Georg Lang and Axel Buchner},
	Journal = {Behav Res Methods},
	Keywords = {Algorithms; Behavioral Sciences; Biomedical Research; Data Interpretation, Statistical; Mathematical Computing; Microcomputers; Sensitivity and Specificity; Social Sciences; Software; Statistics, Nonparametric},
	Month = {May},
	Number = {2},
	Pages = {175--191},
	Pmid = {17695343},
	Timestamp = {2008.01.14},
	Title = {G*Power 3: a flexible statistical power analysis program for the social, behavioral, and biomedical sciences.},
	Volume = {39},
	Year = {2007}}

@article{Feldman2008,
	Author = {Feldman, D. and Weinshall, D.},
	Doi = {10.1109/TPAMI.2007.70766},
	Journal = IEEE_J_PAMI,
	Month = {July},
	Number = {7},
	Pages = {1171--1185},
	Timestamp = {2008.11.26},
	Title = {Motion Segmentation and Depth Ordering Using an Occlusion Detector},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70766}}

@article{Feldmar1999,
	Author = {Jacques Feldmar and Nicholas Ayache},
	Citeseercitationcount = {0},
	Citeseerurl = {http://citeseer.ist.psu.edu/382235.html},
	Timestamp = {2007.09.09},
	Title = {Definition of a 4D continuous planispheric transformation for the tracking and the analysis of LV motion},
	Year = {1999},
	Bdsk-Url-1 = {http://citeseer.ist.psu.edu/382235.html}}

@article{Fetita2004,
	Author = {Catalin I. Fetita and Francoise Preteux and Catherine Beigelman-Aubry and Philippe Grenier},
	Journal = {IEEE Transactions on Medical Imaging},
	Number = {11},
	Owner = {tustison},
	Pages = {1353-1364},
	Title = {Pulmonary Airways: 3-D Reconstruction From Multislice CT and Clinical Investigation},
	Volume = {23},
	Year = {2004}}

@article{Figuerido2000,
	Author = {Mario T. Figuerido and Jose M. N. Leitao and Anil K. Jain},
	Journal = {IEEE Transactions on Image Processing},
	Number = {6},
	Owner = {tustison},
	Pages = {1075-1087},
	Title = {Unsupervised Contour Representation and Estimation Using B-Splines and a Minimum Description Length Criterion},
	Volume = {9},
	Year = {2000}}

@article{Finucane1969,
	Author = {K. E. Finucane and H. J. Colebatch},
	Journal = {J Appl Physiol},
	Keywords = {Asthma; Elasticity; Female; Humans; Lung; Lung Compliance; Male; Pulmonary Emphysema; Respiration; Spirometry},
	Month = {Mar},
	Number = {3},
	Pages = {330--338},
	Pmid = {5773176},
	Timestamp = {2007.09.08},
	Title = {Elastic behavior of the lung in patients with airway obstruction.},
	Volume = {26},
	Year = {1969}}

@article{Fletcher2004,
	Author = {P. Thomas Fletcher and Conglin Lu and Stephen M. Pizer and Sarang Joshi},
	Journal = {IEEE Transactions on Medical Imaging},
	Number = {8},
	Owner = {tustison},
	Pages = {995-1005},
	Title = {Principal Geodesic Analysis for the Study of Nonlinear Statistics of Shape},
	Volume = {23},
	Year = {2004}}

@article{Ford1956,
	Author = {L. R. Ford and D. R. Fulkerson},
	Journal = {Canadian Journal of Mathematics},
	Pages = {399-404},
	Timestamp = {2008.11.14},
	Title = {Maximal flow through a network},
	Volume = {8},
	Year = {1956}}

@article{Forsey1988,
	Author = {David R. Forsey and Richard H. Bartels},
	Journal = {Computer Graphics},
	Number = {4},
	Owner = {tustison},
	Pages = {205-212},
	Title = {Hierarchical B-Spline Refinement},
	Volume = {22},
	Year = {1988}}

@article{Fox2001,
	Author = {N. Fox and W. Crum and R. Scahill and J. Stevens and J. Janssen and M. Rossor},
	Journal = {Lancet},
	Pages = {201-205},
	Title = {Imaging of onset and progression of Alzheimer's disease with voxel-compression mapping of serial magnetic resonance images},
	Volume = {358},
	Year = {2001}}

@article{Frangi2001,
	Author = {A. F. Frangi and W. J. Niessen and M A. Viergever},
	Journal = {IEEE Transactions on Medical Imaging},
	Pages = {2-25},
	Timestamp = {2006.12.20},
	Title = {Three-Dimensional Modeling for Functional Analysis: A Review},
	Volume = {20},
	Year = {2001}}

@inproceedings{Frangi1998,
	Author = {Alejandro F. Frangi and Wiro J. Niessena and Koen L. Vincken and Max A. Viergever},
	Booktitle = {Medical Image Computing and Computer-Assisted Intervention (MICCAI)},
	Owner = {tustison},
	Title = {Multiscale vessel enhancment filtering},
	Year = {1998}}

@article{Frankot1988,
	Author = {Robert T. Frankot and Rama Chellappa},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {4},
	Owner = {tustison},
	Pages = {439-451},
	Title = {A Method for Enforcing Integrability in Shape from Shading Algorithms},
	Volume = {10},
	Year = {1988}}

@article{FFTW05,
	Author = {Frigo, Matteo and Johnson, Steven~G.},
	Journal = {Proceedings of the IEEE},
	Note = {special issue on "Program Generation, Optimization, and Platform Adaptation"},
	Number = {2},
	Pages = {216--231},
	Title = {The Design and Implementation of {FFTW3}},
	Volume = {93},
	Year = {2005}}

@article{Fu2008,
	Author = {Fu, Yun and Yan, Shuicheng and Huang, Thomas S.},
	Doi = {10.1109/TPAMI.2008.154},
	Journal = IEEE_J_PAMI,
	Month = {Dec.},
	Number = {12},
	Pages = {2229--2235},
	Timestamp = {2008.11.26},
	Title = {Correlation Metric for Generalized Feature Extraction},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2008.154}}

@article{Fumera2008,
	Author = {Fumera, G. and Roli, F. and Serrau, A.},
	Doi = {10.1109/TPAMI.2008.30},
	Journal = IEEE_J_PAMI,
	Month = {July},
	Number = {7},
	Pages = {1293--1299},
	Timestamp = {2008.11.26},
	Title = {A Theoretical Analysis of Bagging as a Linear Combination of Classifiers},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2008.30}}

@article{Galant2006,
	Abstract = {BACKGROUND: The current guideline for classifying asthma severity, the National Asthma Education Prevention Program (NAEPP) 2002, is not evidence-based. We had the opportunity to validate this guideline in an untreated inner-city population, both in those < or =5 and those >5 years of age. The basis for this retrospective validation model was to determine how well the NAEPP severity classification based on symptom-frequency criteria alone identified patients in those age groups demonstrating significant morbidity the previous year and thus the potential need for controller therapy. METHODS: Using a mobile asthma van (Breathmobile) at the school site, children not receiving controller medication were evaluated by an asthma specialist for severity according to NAEPP guideline clinical criteria. Validation was determined by the relationship of guideline severity to > or =2 emergency department (ED) visits, any hospitalization, health care utilization (any ED visit, hospitalization), number of exacerbations, and school absenteeism resulting from asthma the prior year. RESULTS: Eight hundred twenty-six asthmatic children were evaluated; 89 (10.8\%) were < or =2 years, 222 (26.9\%) were 3 to 5 years, and 515 (62.3\%) were >5 years of age; 60.5\% were male, and 80.9\% were Hispanic. Classification of asthma severity included 34.4\% with mild intermittent, 10.2\% with mild persistent, 31.5\% with moderate persistent, and 24.0\% with severe persistent asthma categories. There were significantly more Hispanic children and children < or =5 years classified as having mild intermittant asthma. Morbidity was clearly related to severity in the overall population. However, although the health care utilization was significantly related to severity, it was borderline in those 3 to 5 years and nonsignificant in children < or =2 years. CONCLUSIONS: The NAEPP guidelines 2002, based on symptom-frequency criteria as assessed in this study, seem to offer a valid basis for classifying asthma severity in those >5 years of age but may underclassify younger children. Our data suggest that morbidity experienced in the prior year may provide a useful additional criterion for classifying asthma severity, particularly in those children < or =5 years of age.},
	Author = {Stanley P Galant and Tricia Morphew and Silvia Amaro and Otto Liao},
	Doi = {10.1542/peds.2005-1076},
	Journal = {Pediatrics},
	Keywords = {Asthma; Child; Child, Preschool; Female; Humans; Male; Practice Guidelines; Respiratory Function Tests; School Health Services; Severity of Illness Index},
	Month = {Apr},
	Number = {4},
	Pages = {1038--1045},
	Pii = {117/4/1038},
	Pmid = {16585297},
	Timestamp = {2007.09.08},
	Title = {Current asthma guidelines may not identify young children who have experienced significant morbidity.},
	Url = {http://dx.doi.org/10.1542/peds.2005-1076},
	Volume = {117},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1542/peds.2005-1076}}

@article{Galloway1975,
	Author = {M. M. Galloway},
	Journal = {Computer Graphics and Image Processing},
	Pages = {172-179},
	Timestamp = {2008.05.26},
	Title = {Texture Analysis Using Gray Level Run Lengths},
	Volume = {4},
	Year = {1975}}

@article{Garcia2004,
	Author = {Garcia, C. and Delakis, M.},
	Doi = {10.1109/TPAMI.2004.97},
	Journal = IEEE_J_PAMI,
	Month = {Nov.},
	Number = {11},
	Pages = {1408--1423},
	Timestamp = {2008.11.26},
	Title = {Convolutional face finder: a neural architecture for fast and robust face detection},
	Volume = {26},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2004.97}}

@article{Garot2000,
	Abstract = {BACKGROUND: Tagged MRI of the heart is difficult to implement clinically because of the lack of fast analytical techniques. We investigated the accuracy of harmonic phase (HARP) imaging for rapid quantification of myocardial strains and for detailed analysis of left ventricular (LV) function during dobutamine stimulation. METHODS AND RESULTS: Tagged MRI was performed in 10 volunteers at rest and during 5 to 20 microg(-1). kg(-1). min(-1) dobutamine and in 9 postinfarct patients at rest. We compared 2D myocardial strains (circumferential shortening, Ecc; maximal shortening, E(2); and E(2), direction) as assessed by a conventional technique and by HARP. Full quantitative analysis of the data was 10 times faster with HARP. For pooled data, the regression coefficient was r=0.93 for each strain (P<0.001). In volunteers, Ecc and E(2) were greater in the free wall than in the septum (P<0.01), but recruitable myocardial strain at peak dobutamine was greater in the LV septum (P<0.01). E(2) orientation shifted away from the circumferential direction at peak dobutamine (P<0.01). HARP accurately detected subtle changes in myocardial strain fields under increasing doses of dobutamine. In patients, HARP-determined Ecc and E(2) values were dramatically reduced in the asynergic segments as compared with remote (P<0.001), and E(2) direction shifted away from the circumferential direction (P<0.001). CONCLUSIONS: HARP MRI provides fast, accurate assessment of myocardial strains from tagged MR images in normal subjects and in patients with coronary artery disease with wall motion abnormalities. HARP correctly indexes dobutamine-induced changes in strains and has the potential for on-line quantitative monitoring of LV function during stress testing.},
	Author = {J. Garot and D. A. Bluemke and N. F. Osman and C. E. Rochitte and E. R. McVeigh and E. A. Zerhouni and J. L. Prince and J. A. Lima},
	Journal = {Circulation},
	Keywords = {Adult; Coronar; Dobutamine; Female; Heart; Heart Septum; Humans; Magnetic Resonance Imaging; Male; Middle Aged; Myocardial Contraction; Myocardium; Reference Values; Stress, Mechanical; Time Factors; y Disease},
	Month = {Mar},
	Number = {9},
	Pages = {981--988},
	Pmid = {10704164},
	Timestamp = {2007.09.09},
	Title = {Fast determination of regional myocardial strain fields from tagged cardiac images using harmonic phase MRI.},
	Volume = {101},
	Year = {2000}}

@article{Gattinoni1988,
	Author = {L. Gattinoni and A. Pesenti and M. Bombino and S. Baglioni and M. Rivolta and F. Rossi and G. Rossi and R. Fumagalli and R. Marcolin and D. Mascheroni},
	Journal = {Anesthesiology},
	Month = {Dec},
	Number = {6},
	Pages = {824--832},
	Timestamp = {2009.05.18},
	Title = {Relationships between lung computed tomographic density, gas exchange, and PEEP in acute respiratory failure.},
	Volume = {69},
	Year = {1988}}

@inproceedings{Gee2006,
	Author = {J.C. Gee and T.A. Sundaram and B. Avants and P. Burstein and P. Yushkevich and H. Zhang and I. Casselbrini and P. Akeson and G. Pettersson and B. Wyman and B. Peterson},
	Booktitle = {Proc. of the 14th Annual Meeting of ISMRM},
	Pages = {1326},
	Timestamp = {2009.05.18},
	Title = {Quantitation of pulmonary structure via registration and normalization of serial {3He} {MR} images},
	Year = {2006}}

@article{Gee2003,
	Abstract = {RATIONALE AND OBJECTIVES: The aim of this study was to investigate a method for quantifying lung motion from the registration of successive images in serial magnetic resonance imaging acquisitions during normal respiration. MATERIALS AND METHODS: Estimates of pulmonary motion were obtained by summing the normalized cross-correlation over serially acquired lung images to identify corresponding locations between the images. The estimated motions were modeled as deformations of an elastic body and thus reflect to a first order approximation the true physical behavior of lung parenchyma. The Lagrangian strain, derived from the calculated motion fields, were used to quantify the tissue deformation induced in the lung over the serial acquisition. RESULTS: The method was validated on a magnetic resonance imaging study, for which breath-hold images were acquired of a healthy volunteer at different phases of the respiratory cycle. Regional parenchymal strain was observed to be oriented toward the pulmonary hilum, with strain magnitude maximal at the midcycle of the expiratory phase. CONCLUSION: In vivo magnetic resonance imaging quantification of lung motion holds the potential of providing a new diagnostic dimension in the assessment of pulmonary function, augmenting the information provided by studies of ventilation and perfusion.},
	Author = {James Gee and Tessa Sundaram and Ichiro Hasegawa and Hidemasa Uematsu and Hiroto Hatabu},
	Journal = {Acad Radiol},
	Keywords = {Adult; Biomechanics; Humans; Lung; Magnetic Resonance Imaging; Male; Movement; Respiratory Mechanics},
	Month = {Oct},
	Number = {10},
	Pages = {1147--1152},
	Pmid = {14587632},
	Timestamp = {2007.09.09},
	Title = {Characterization of regional pulmonary mechanics from serial magnetic resonance imaging data.},
	Volume = {10},
	Year = {2003}}

@article{Gee1999,
	Author = {James C. Gee},
	Journal = {Pattern Recognition},
	Owner = {tustison},
	Title = {On Matching Brain Volumes},
	Volume = {32},
	Year = {1999}}

@inbook{Gee1999a,
	Author = {James C. Gee and David R. Haynor},
	Chapter = {Numerical Methods for High-Dimensional Warps},
	Editor = {Arthur W. Toga},
	Owner = {tustison},
	Pages = {101-114},
	Publisher = {Academic Press},
	Title = {Brain Warping},
	Year = {1999}}

@article{Geiger1995,
	Author = {Davi Geiger and Alok Gupta and Luiz A. Costa and John Vlontzos},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {3},
	Owner = {tustison},
	Pages = {294-302},
	Title = {Dynamic Programming for Detecting, Tracking, and Matching Deformable Contours},
	Volume = {17},
	Year = {1995}}

@article{Geiger2003,
	Author = {Geiger, D. and Tyng-Luh Liu and Kohn, R.V.},
	Doi = {10.1109/TPAMI.2003.1159948},
	Journal = IEEE_J_PAMI,
	Month = {Jan.},
	Number = {1},
	Pages = {86--99},
	Timestamp = {2008.11.26},
	Title = {Representation and self-similarity of shapes},
	Volume = {25},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2003.1159948}}

@article{Gelb2008,
	Abstract = {PURPOSE OF REVIEW: This review examines the physiologic mechanisms responsible for persistent maximum expiratory airflow limitation in nonsmoking patients with acute and chronic moderate to severe persistent asthma in comparison to chronic obstructive pulmonary disease. RECENT FINDINGS: The phenomenon of acute but reversible loss of lung elastic recoil during acute asthma is reviewed, although no plausible pathophysiologic explanation has been offered. Nonsmoking adults with stable asthma and persistent maximum expiratory airflow limitation, despite optimal polytherapy, were shown to have unsuspected and unexplained marked loss of lung elastic recoil in the absence of lung computed tomography scored emphysema. This condition resulted in up to 50\% reduction in maximum expiratory airflow. Furthermore, these patients remain at high risk for adverse clinical events, including near-fatal asthma. In chronic obstructive pulmonary disease, reduction in maximum expiratory airflow is related to variable extent of loss of lung elastic recoil secondary to emphysema and concurrent intrinsic airway obstruction or obliteration of small airways. There is also an unexplained loss of lung elastic recoil in primary intrinsic small airways disease in the absence of emphysema. SUMMARY: Nonsmoking patients with moderate-severe persistent asthma and patients with smoking-related chronic obstructive pulmonary disease share similar physiologic mechanisms of expiratory airflow limitation, but probably caused by different anatomic abnormalities.},
	Author = {Arthur Gelb and Noe Zamel and Anita Krishnan},
	Doi = {10.1097/MCP.0b013e3282f197df},
	Journal = {Curr Opin Pulm Med},
	Month = {Jan},
	Number = {1},
	Pages = {24--30},
	Pii = {00063198-200801000-00006},
	Pmid = {18043272},
	Timestamp = {2007.12.20},
	Title = {Physiologic similarities and differences between asthma and chronic obstructive pulmonary disease.},
	Url = {http://dx.doi.org/10.1097/MCP.0b013e3282f197df},
	Volume = {14},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1097/MCP.0b013e3282f197df}}

@article{Gelb2002,
	Abstract = {STUDY OBJECTIVES: To investigate the progression and mechanism(s) for fixed maximum expiratory airflow (max) limitation in patients with chronic persistent asthma. METHODS: When optimally treated and in clinically stable condition, we studied 21 asthmatic patients and classified them into three groups based on the severity of expiratory airflow limitation: (1) group A included 5 asthmatic patients (four women; mean +/- SD age, 51 +/- 17 years) with mild persistent asthma (FEV(1) > 80\% predicted) with serial FEV(1) measurements obtained prior to the present study for 16 +/- 4 years; (2) group B included 11 asthmatic patients (three women; mean age, 64 +/- 11 years) with moderate persistent asthma (FEV(1) of 60 to 80\% predicted) with serial FEV(1) measurements for 12 +/- 4 years; and (3) group C included 5 asthmatic patients (three women; mean age, 55 +/- 16 years) with severe persistent asthma (FEV(1) < 60\% predicted) with serial FEV(1) measurements for 11 plus minus 5 years. RESULTS: Lung CT indicated no or trivial emphysema, and diffusion was normal in all asthmatics. There was a marked loss of lung elastic recoil at total lung capacity (TLC) in all asthmatic patients in group B (16 +/- 4 cm H(2)O) and group C (15 +/- 5 cm H(2)O), but none or minimal in group A (22 +/- 1 cm H(2)O) [p < 0.01], and loss of elastic recoil accounted for 34\% and 50\% of decreased maximal expiratory airflow (max) at 80\% and 70\% TLC, respectively. Comparison with previous longitudinal data indicated individual asthmatics when in clinically stable condition remained predominantly in the same FEV(1) percent predicted classification group as in the current study. CONCLUSION: Patients with chronic moderate and severe persistent asthma, despite optimal therapy, have reduced max for many years in part due to (early?) loss of lung elastic recoil from unknown mechanism(s). This challenges current concept of airway remodeling.},
	Author = {Arthur F Gelb and Jesse Licuanan and Chris M Shinar and Noe Zamel},
	Journal = {Chest},
	Keywords = {Aged; Asthma; Chronic Disease; Elasticity; Female; Humans; Lung; Male; Maximal Expiratory Flow Rate; Middle Aged; Pulmonary Diffusing Capacity; Retrospective Studies; Total Lung Capacity},
	Month = {Mar},
	Number = {3},
	Pages = {715--721},
	Pmid = {11888951},
	Timestamp = {2007.09.08},
	Title = {Unsuspected loss of lung elastic recoil in chronic persistent asthma.},
	Volume = {121},
	Year = {2002}}

@article{Gelb2002a,
	Abstract = {This review emphasizes the mechanisms responsible for maximum expiratory airflow limitation in acute and chronic persistent asthma. The phenomenon of acute but reversible loss of lung elastic recoil during acute asthma is reviewed, although no plausible physiologic explanations are offered. The authors have recently studied adult chronic, stable asthmatics with persistent forced expiratory volume in 1 second less than 80\% predicted, despite optimal polytherapy. The asthmatics had unsuspected marked loss of lung elastic recoil in the absence of emphysema that was responsible for a 32 to 35\% reduction in maximum expiratory airflow at 80\% total lung capacity and a 28 to 60\% reduction in maximum expiratory airflow at 70\% total lung capacity. Work in progress indicates that persistent reduced maximum expiratory airflow may be present for at least 12 +/- 4 years (mean +/- SD) and suggests possible early loss of lung elastic recoil. These observations provide a challenge to the concept of intrinsic airway narrowing resulting from airway remodeling as the major cause of expiratory maximum expiratory airflow limitation in chronic, moderate asthma and severe, persistent asthma. No morphologic or physiologic abnormalities readily explain the chronic, persistent loss of lung recoil.},
	Author = {Arthur F Gelb and Noe Zamel},
	Journal = {Curr Opin Pulm Med},
	Keywords = {Acute Disease; Asthma; Chronic Disease; Elasticity; Humans; Lung; Respiratory Mechanics; Respiratory Muscles; Spirometry},
	Month = {Jan},
	Number = {1},
	Pages = {50--53},
	Pmid = {11753124},
	Timestamp = {2007.09.08},
	Title = {Lung elastic recoil in acute and chronic asthma.},
	Volume = {8},
	Year = {2002}}

@book{Gell-Mann2004,
	Author = {M. Gell-Mann and C. Tsallis},
	Publisher = {Oxford University Press},
	Timestamp = {2008.08.14},
	Title = {Nonextensive Entropy},
	Year = {2004}}

@inproceedings{Geng2005,
	Author = {Xiujuan Geng and Dinesh Kumar and Gary E. Christensen},
	Booktitle = {Proceedings 19th International Conference on Information Processing in Medical Imaging},
	Owner = {tustison},
	Pages = {468-479},
	Title = {Transitive Inverse-Consistent Manifold Registration},
	Year = {2005}}

@article{Geskin1998,
	Abstract = {BACKGROUND: The assessment of return of function within dysfunctional myocardium after acute myocardial infarction (MI) using contractile reserve has been primarily qualitative. Magnetic resonance (MR) myocardial tagging is a novel noninvasive method that measures intramyocardial function. We hypothesized that MR tagging could be used to quantify the intramyocardial response to low-dose dobutamine and relate this response to return of function in patients after first MI. METHODS AND RESULTS: Twenty patients with a first reperfused MI (age, 53+/-12 years; 16 male; 11 inferior MIs) were studied. Patients underwent breath-hold MR-tagged short-axis imaging on day 4+/-2 after MI at baseline and during dobutamine infusion at 5 and 10 microg x kg(-1) x min(-1). At 8+/-1 weeks after MI, patients returned for a follow-up MR tagging study without dobutamine. Quantification of percent intramyocardial circumferential segment shortening (\%S) was performed. Low-dose dobutamine MRI was well tolerated. Overall, mean \%S was 15+/-11\% at baseline (n=227 segments), increased to 16+/-10\% at 5 microg x kg(-1) x min(-1) dobutamine (P=NS), 21+/-10\% at peak (P<0.0001 versus baseline and 5 microg x kg(-1) x min(-1), and 18+/-10\% at 8 weeks (P<0.004 versus baseline and peak). The increase in \%S with peak dobutamine was greater in dysfunctional myocardium (103 segments, +9+/-10\%) than in normal tissue (124 segments, +4+/-12\%, P<0.0001). In dysfunctional regions, \%S also increased from 6+/-7\% at baseline to 14+/-10\% at 8 weeks after MI (P<0.0001). In dysfunctional regions that responded normally to peak dobutamine (> or =5\% increase in \%S), the increase in \%S from baseline to 8 weeks after MI (+9+/-9\%) was greater than in those regions that did not respond normally (+5+/-9\%, P<0.04). Midmyocardial and subepicardial response to dobutamine were predictive of functional recovery, but the subendocardial response was not. CONCLUSIONS: The response of intramyocardial function to low-dose dobutamine after reperfused MI can be quantified with MR tagging. Dysfunctional tissue after MI demonstrates a larger contractile response to dobutamine than normal myocardium. A normal increase in shortening elicited by dobutamine within dysfunctional midwall and subepicardium predicts greater functional recovery at 8 weeks after MI, but the response within the subendocardium is not predictive.},
	Author = {G. Geskin and C. M. Kramer and W. J. Rogers and T. M. Theobald and D. Pakstis and Y. L. Hu and N. Reichek},
	Journal = {Circulation},
	Keywords = {Adult; Aged; Dobutamine; Female; Heart; Humans; Magnetic Resonance Imaging; Male; Middle Aged; Myocardial Contraction; Myocardial Infarction},
	Month = {Jul},
	Number = {3},
	Pages = {217--223},
	Pmid = {9697821},
	Timestamp = {2007.09.09},
	Title = {Quantitative assessment of myocardial viability after infarction by dobutamine magnetic resonance tagging.},
	Volume = {98},
	Year = {1998}}

@article{Gevenois1996,
	Author = {P. A. Gevenois and P. De Vuyst and M. Sy and P. Scillia and L. Chaminade and V. de Maertelaer and J. Zanen and J. C. Yernault},
	Journal = {Radiology},
	Month = {Jun},
	Number = {3},
	Pages = {825--829},
	Timestamp = {2009.05.18},
	Title = {Pulmonary emphysema: quantitative {CT} during expiration.},
	Volume = {199},
	Year = {1996}}

@article{Gevenois1995,
	Author = {P. A. Gevenois and J. C. Yernault},
	Journal = {Eur Respir J},
	Month = {May},
	Number = {5},
	Pages = {843--848},
	Timestamp = {2009.05.18},
	Title = {Can computed tomography quantify pulmonary emphysema?},
	Volume = {8},
	Year = {1995}}

@article{Giblin2004,
	Author = {Giblin, P. and Kimia, B.B.},
	Doi = {10.1109/TPAMI.2004.1262192},
	Journal = IEEE_J_PAMI,
	Month = {Feb.},
	Number = {2},
	Pages = {238--251},
	Timestamp = {2008.11.26},
	Title = {A formal classification of 3D medial axis points and their local geometry},
	Volume = {26},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2004.1262192}}

@article{Giblin2003,
	Author = {Giblin, P.J. and Kimia, B.B.},
	Doi = {10.1109/TPAMI.2003.1206518},
	Journal = IEEE_J_PAMI,
	Month = {July},
	Number = {7},
	Pages = {895--911},
	Timestamp = {2008.11.26},
	Title = {On the intrinsic reconstruction of shape from its symmetries},
	Volume = {25},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2003.1206518}}

@article{Gierada2001,
	Author = {D. S. Gierada and R. D. Yusen and T. K. Pilgram and L. Crouch and R. M. Slone and K. T. Bae and S. S. Lefrak and J. D. Cooper},
	Journal = {Radiology},
	Month = {Aug},
	Number = {2},
	Pages = {448--454},
	Timestamp = {2009.05.18},
	Title = {Repeatability of quantitative {CT} indexes of emphysema in patients evaluated for lung volume reduction surgery.},
	Volume = {220},
	Year = {2001}}

@article{Gilboa2008,
	Author = {Gilboa, Guy},
	Doi = {10.1109/TPAMI.2008.23},
	Journal = IEEE_J_PAMI,
	Month = {Dec.},
	Number = {12},
	Pages = {2175--2187},
	Timestamp = {2008.11.26},
	Title = {Nonlinear Scale Space with Spatially Varying Stopping Time},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2008.23}}

@article{Gilman1983,
	Author = {M. J. Gilman and R. G. Laurens and J. W. Somogyi and E. G. Honig},
	Journal = {J Comput Assist Tomogr},
	Month = {Jun},
	Number = {3},
	Pages = {407--410},
	Timestamp = {2009.05.18},
	Title = {{CT} attenuation values of lung density in sarcoidosis.},
	Volume = {7},
	Year = {1983}}

@article{Girolami2003,
	Author = {Girolami, M. and Chao He},
	Doi = {10.1109/TPAMI.2003.1233899},
	Journal = IEEE_J_PAMI,
	Month = {Oct.},
	Number = {10},
	Pages = {1253--1264},
	Timestamp = {2008.11.26},
	Title = {Probability density estimation from optimally condensed data samples},
	Volume = {25},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2003.1233899}}

@article{Gold1998,
	Author = {Steven Gold and Anand Rangarajan and Chien-Ping Lu and Suguna Pappu and Eric Mjolsness},
	Journal = {Pattern Recognition},
	Number = {8},
	Pages = {1019-1031},
	Timestamp = {2007.10.23},
	Title = {New Algorithms for {2D} and {3D} Point Matching: Pose Estimation and Correspondence},
	Volume = {31},
	Year = {1998}}

@article{Goldentahal2004,
	Author = {Rony Goldentahal and Michel Bercovier},
	Journal = {Computing},
	Number = {72},
	Owner = {tustison},
	Pages = {53-64},
	Title = {Spline Curve Approximation and Design by Optimal Control Over the Knots},
	Year = {2004}}

@article{Goldin2004,
	Author = {Jonathan G Goldin},
	Journal = {J Thorac Imaging},
	Month = {Oct},
	Number = {4},
	Pages = {235--240},
	Timestamp = {2009.05.18},
	Title = {Quantitative {CT} of emphysema and the airways.},
	Volume = {19},
	Year = {2004}}

@article{Goldin2002,
	Author = {Jonathan G Goldin},
	Journal = {Radiol Clin North Am},
	Month = {Jan},
	Number = {1},
	Pages = {145--162},
	Timestamp = {2009.05.18},
	Title = {Quantitative {CT} of the lung.},
	Volume = {40},
	Year = {2002}}

@article{Golub1999,
	Author = {Gene H. Golub and Per Christian Hansen and Dianne P. O'Leary},
	Journal = {SIAM Journal on Matrix Analysis and Applications},
	Number = {1},
	Owner = {tustison},
	Pages = {185-194},
	Title = {Tikhonov Regularization and Total Least Squares},
	Volume = {21},
	Year = {1999}}

@article{Goshen2008,
	Author = {Goshen, L. and Shimshoni, H.},
	Doi = {10.1109/TPAMI.2007.70768},
	Journal = IEEE_J_PAMI,
	Month = {July},
	Number = {7},
	Pages = {1230--1242},
	Timestamp = {2008.11.26},
	Title = {Balanced Exploration and Exploitation Model Search for Efficient Epipolar Geometry Estimation},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70768}}

@article{Gould1988,
	Author = {G. A. Gould and W. MacNee and A. McLean and P. M. Warren and A. Redpath and J. J. Best and D. Lamb and D. C. Flenley},
	Journal = {Am Rev Respir Dis},
	Month = {Feb},
	Number = {2},
	Pages = {380--392},
	Timestamp = {2009.05.18},
	Title = {{CT} measurements of lung density in life can quantitate distal airspace enlargement--an essential defining feature of human emphysema.},
	Volume = {137},
	Year = {1988}}

@article{Graham2000,
	Author = {S. M. Graham and G. McLennan and G. F. Funk and H. T. Hoffman and T. M. McCulloch and J. Cook-Granroth and E. A. Hoffman},
	Journal = {Am J Otolaryngol},
	Number = {4},
	Pages = {263--270},
	Timestamp = {2009.05.18},
	Title = {Preoperative assessment of obstruction with computed tomography image analysis.},
	Volume = {21},
	Year = {2000}}

@article{Gramkow2001,
	Author = {Claus Gramkow},
	Journal = {Journal of Mathematical Imaging and Vision},
	Owner = {tustison},
	Pages = {7-16},
	Title = {On Averaging Rotations},
	Volume = {15},
	Year = {2001}}

@article{Greig1989,
	Author = {D. M. Greig and B. T. Porteous and A. H. Seheult},
	Journal = {J. R. Statist. Soc. B},
	Number = {2},
	Owner = {tustison},
	Pages = {271-279},
	Title = {Exact Maximum A Posteriori Estimation for Binary Images},
	Volume = {51},
	Year = {1989}}

@article{Greiner1994,
	Author = {Gunther Greiner and Hans-Peter Seidel},
	Journal = {IEEE Computer Graphics and Applications},
	Number = {2},
	Owner = {tustison},
	Pages = {56-60},
	Title = {Modeling with Triangular B-Splines},
	Volume = {14},
	Year = {1994}}

@article{Grenier2002,
	Journal = {Eur Radiol},
	Month = {May},
	Number = {5},
	Pages = {1022--1044},
	Timestamp = {2009.05.18},
	Title = {New frontiers in {CT} imaging of airway disease.},
	Volume = {12},
	Year = {2002}}

@article{Guerrero2006,
	Abstract = {A novel method for dynamic ventilation imaging of the full respiratory cycle from four-dimensional computed tomography (4D CT) acquired without added contrast is presented. Three cases with 4D CT images obtained with respiratory gated acquisition for radiotherapy treatment planning were selected. Each of the 4D CT data sets was acquired during resting tidal breathing. A deformable image registration algorithm mapped each (voxel) corresponding tissue element across the 4D CT data set. From local average CT values, the change in fraction of air per voxel (i.e. local ventilation) was calculated. A 4D ventilation image set was calculated using pairs formed with the maximum expiration image volume, first the exhalation then the inhalation phases representing a complete breath cycle. A preliminary validation using manually determined lung volumes was performed. The calculated total ventilation was compared to the change in contoured lung volumes between the CT pairs (measured volume). A linear regression resulted in a slope of 1.01 and a correlation coefficient of 0.984 for the ventilation images. The spatial distribution of ventilation was found to be case specific and a 30\% difference in mass-specific ventilation between the lower and upper lung halves was found. These images may be useful in radiotherapy planning.},
	Author = {Thomas Guerrero and Kevin Sanders and Edward Castillo and Yin Zhang and Luc Bidaut and Tinsu Pan and Ritsuko Komaki},
	Doi = {10.1088/0031-9155/51/4/002},
	Journal = {Phys Med Biol},
	Keywords = {Algor; Humans; Imaging, Three-Dimensional; Lung; Pulmonary Ventilation; Radiographic Image Enhancement; Radiographic Image Interpretation, Computer-Assisted; Reproducibility of Res; Sensitivity and Specificity; Subtraction Technique; Tidal Volume; Tomography, X-Ray Computed; ithms; ults},
	Month = {Feb},
	Number = {4},
	Pages = {777--791},
	Pii = {S0031-9155(06)04227-8},
	Pmid = {16467578},
	Timestamp = {2007.09.09},
	Title = {Dynamic ventilation imaging from four-dimensional computed tomography.},
	Url = {http://dx.doi.org/10.1088/0031-9155/51/4/002},
	Volume = {51},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1088/0031-9155/51/4/002}}

@inbook{Guo2005,
	Author = {H. Guo and A. Rangarajan and S. Joshi},
	Chapter = {Diffeomorphic Point Matching},
	Pages = {205-220},
	Publisher = {Springer},
	Timestamp = {2008.09.04},
	Title = {Handbook of Mathematical Models in Computer Vision},
	Year = {2005}}

@article{Hagemann1999,
	Abstract = {The accuracy of image-guided neurosurgery generally suffers from brain deformations due to intraoperative changes. These deformations cause significant changes of the anatomical geometry (organ shape and spatial interorgan relations), thus making intraoperative navigation based on preoperative images error prone. In order to improve the navigation accuracy, we developed a biomechanical model of the human head based on the finite element method, which can be employed for the correction of preoperative images to cope with the deformations occurring during surgical interventions. At the current stage of development, the two-dimensional (2-D) implementation of the model comprises two different materials, though the theory holds for the three-dimensional (3-D) case and is capable of dealing with an arbitrary number of different materials. For the correction of a preoperative image, a set of homologous landmarks must be specified which determine correspondences. These correspondences can be easily integrated into the model and are maintained throughout the computation of the deformation of the preoperative image. The necessary material parameter values have been determined through a comprehensive literature study. Our approach has been tested for the case of synthetic images and yields physically plausible deformation results. Additionally, we carried out registration experiments with a preoperative MR image of the human head and a corresponding postoperative image simulating an intraoperative image. We found that our approach yields good prediction results, even in the case when correspondences are given in a relatively small area of the image only.},
	Author = {A Hagemann and K Rohr and HS Stiehl and U Spetzger and JM Gilsbach},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Biomechanics, Brain, Elasticity, Finite Element Analysis, Humans, Intraoperative Period, Magnetic Resonance Imaging, Models, Neurological, Neurosurgical Procedures, Research Support, Non-U.S. Gov't, Skull, 10628947},
	Month = {Oct},
	Number = {10},
	Owner = {tustison},
	Pages = {875-84},
	Title = {Biomechanical modeling of the human head for physically based, nonrigid image registration.},
	Volume = {18},
	Year = {1999}}

@article{Han2008,
	Author = {Bohyung Han and Comaniciu, D. and Ying Zhu and Davis, L.S.},
	Doi = {10.1109/TPAMI.2007.70771},
	Journal = IEEE_J_PAMI,
	Month = {July},
	Number = {7},
	Pages = {1186--1197},
	Timestamp = {2008.11.26},
	Title = {Sequential Kernel Density Approximation and Its Application to Real-Time Visual Tracking},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70771}}

@article{Han2001,
	Author = {Chao Han and Thomas S. Hatsukami and Jenq-Neng Hwang and Chun Yuan},
	Journal = {IEEE Transactions on Image Processing},
	Number = {6},
	Owner = {tustison},
	Pages = {865-873},
	Title = {A Fast Minimal Path Active Contour Model},
	Volume = {10},
	Year = {2001}}

@article{Haralick1973,
	Author = {Robert M. Haralick and K. Shanmugam and Itshak Dinstein},
	Journal = {IEEE Transactions on Systems, Man, and Cybernetics},
	Number = {6},
	Pages = {610-621},
	Timestamp = {2009.01.23},
	Title = {Textural Features for Image Classification},
	Volume = {3},
	Year = {1973}}

@article{Hasegawa2003,
	Author = {Ichiro Hasegawa and Hidemasa Uematsu and James C Gee and Peter Rogelj and Hee Kwon Song and Masashi Nakatsu and Masaya Takahashi and Warren B Gefter and Hiroto Hatabu},
	Journal = {Acad Radiol},
	Month = {Oct},
	Number = {10},
	Pages = {1091--1096},
	Timestamp = {2009.05.18},
	Title = {Voxelwise mapping of magnetic resonance ventilation-perfusion ratio in a porcine model by multimodality registration: technical note.},
	Volume = {10},
	Year = {2003}}

@inproceedings{Hatabu2001,
	Author = {H. Hatabu and Y. Ohno and H. Uematsu and M. Nakatsu and K. Oshio and W.B. Gefter and J.C. Gee},
	Booktitle = {Proc. of the 9th Annual Meeting of ISMRM},
	Pages = {2008},
	Timestamp = {2009.05.18},
	Title = {A novel imaging method of lung biomechanics via non-rigid registration of serial {MR} images},
	Year = {2001}}

@article{Hatabu2001a,
	Author = {H. Hatabu and Y. Ohno and H. Uematsu and K. Oshio and W.B. Gefter and J. C. Gee},
	Journal = {Radiology},
	Pages = {630},
	Timestamp = {2009.05.18},
	Title = {Lung biomechanics via non-rigid registration of serial {MR} images},
	Volume = {221(P)},
	Year = {2001}}

@article{Havrda1967,
	Author = {M. Havrda and F. Charvat},
	Journal = {Kybernetica},
	Pages = {30-35},
	Timestamp = {2008.09.04},
	Title = {Quantification method of classification processes: concept of structural alpha-entropy},
	Volume = {3},
	Year = {1967}}

@book{Hedges1985,
	Author = {L. V. Hedges and I. Olkin},
	Publisher = {Academic Press},
	Timestamp = {2008.01.14},
	Title = {Statistical Methods for Meta Analysis},
	Year = {1985}}

@article{Hellier2003,
	Abstract = {Although numerous methods to register brains of different individuals have been proposed, no work has been done, as far as we know, to evaluate and objectively compare the performances of different nonrigid (or elastic) registration methods on the same database of subjects. In this paper, we propose an evaluation framework, based on global and local measures of the relevance of the registration. We have chosen to focus more particularly on the matching of cortical areas, since intersubject registration methods are dedicated to anatomical and functional normalization, and also because other groups have shown the relevance of such registration methods for deep brain structures. Experiments were conducted using 6 methods on a database of 18 subjects. The global measures used show that the quality of the registration is directly related to the transformation's degrees of freedom. More surprisingly, local measures based on the matching of cortical sulci did not show significant differences between rigid and non rigid methods.},
	Author = {P Hellier and C Barillot and I Corouge and B Gibaud and G Le Goualher and DL Collins and A Evans and G Malandain and N Ayache and GE Christensen and HJ Johnson},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Adult, Brain, Cerebral Cortex, Comparative Study, Databases, Factual, Humans, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Magnetic Resonance Imaging, Male, Pattern Recognition, Automated, Reproducibility of Results, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, P.H.S., Retrospective Studies, Sensitivity and Specificity, Signal Processing, Computer-Assisted, Single-Blind Method, Subtraction Technique, 12956267},
	Month = {Sep},
	Number = {9},
	Owner = {tustison},
	Pages = {1120-30},
	Title = {Retrospective evaluation of intersubject brain registration.},
	Volume = {22},
	Year = {2003}}

@article{Heremans1992,
	Author = {A. Heremans and J. A. Verschakelen and L. Van fraeyenhoven and M. Demedts},
	Journal = {Chest},
	Month = {Sep},
	Number = {3},
	Pages = {805--811},
	Timestamp = {2009.05.18},
	Title = {Measurement of lung density by means of quantitative {CT} scanning. A study of correlations with pulmonary function tests.},
	Volume = {102},
	Year = {1992}}

@article{Hermosillo2002,
	Author = {Hermosillo, G. and Chef d'Hotel, C. and Faugeras, O.D.},
	Journal = {International Journal of Computer Vision},
	Month = {December},
	Number = {3},
	Pages = {329-343},
	Title = {Variational Methods for Multimodal Image Matching},
	Volume = {50},
	Year = {2002}}

@article{Hersh2007,
	Author = {Craig P Hersh and Francine L Jacobson and Ritu Gill and Edwin K Silverman},
	Journal = {COPD},
	Month = {Dec},
	Number = {4},
	Pages = {331--337},
	Timestamp = {2009.05.18},
	Title = {Computed tomography phenotypes in severe, early-onset chronic obstructive pulmonary disease.},
	Volume = {4},
	Year = {2007}}

@article{Hesselink2008,
	Author = {Hesselink, Wim H. and Roerdink, Jos B.T.M.},
	Doi = {10.1109/TPAMI.2008.21},
	Journal = IEEE_J_PAMI,
	Month = {Dec.},
	Number = {12},
	Pages = {2204--2217},
	Timestamp = {2008.11.26},
	Title = {Euclidean Skeletons of Digital Image and Volume Data in Linear Time by the Integer Medial Axis Transform},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2008.21}}

@article{Hill2004,
	Author = {C. Hill and E. J. R. Van Beek},
	Journal = {Imaging},
	Pages = {61-70},
	Timestamp = {2007.06.06},
	Title = {{MRI} of the chest: present and future},
	Volume = {16},
	Year = {2004}}

@techreport{Hjelle2001a,
	Author = {Oyvind Hjelle},
	Owner = {tustison},
	Title = {Approximation of Scattered Data with Multilevel B-splines},
	Year = {2001}}

@article{Hoffman2004,
	Author = {Eric A Hoffman and Anne V Clough and Gary E Christensen and Ching-Long Lin and Geoffrey McLennan and Joseph M Reinhardt and Brett A Simon and Milan Sonka and Merryn H Tawhai and Edwin J R van Beek and Ge Wang},
	Journal = {Acad Radiol},
	Month = {Dec},
	Number = {12},
	Pages = {1370--1380},
	Timestamp = {2009.05.18},
	Title = {The comprehensive imaging-based analysis of the lung: a forum for team science.},
	Volume = {11},
	Year = {2004}}

@article{Hoffman2003,
	Author = {Eric A Hoffman and Joseph M Reinhardt and Milan Sonka and Brett A Simon and Junfeng Guo and Osama Saba and Deokiee Chon and Shaher Samrah and Hidenori Shikata and Juerg Tschirren and Kalman Palagyi and Kenneth C Beck and Geoffrey McLennan},
	Journal = {Acad Radiol},
	Month = {Oct},
	Number = {10},
	Pages = {1104--1118},
	Timestamp = {2009.05.18},
	Title = {Characterization of the interstitial lung diseases via density-based and texture-based analysis of computed tomography images of lung structure and function.},
	Volume = {10},
	Year = {2003}}

@article{Hoffman2006,
	Author = {Eric A Hoffman and Brett A Simon and Geoffrey McLennan},
	Journal = {Proc Am Thorac Soc},
	Month = {Aug},
	Number = {6},
	Pages = {519--532},
	Timestamp = {2009.05.18},
	Title = {State of the Art. A structural and functional assessment of the lung via multidetector-row computed tomography: phenotyping chronic obstructive pulmonary disease.},
	Volume = {3},
	Year = {2006}}

@inbook{Hollig2002,
	Author = {Klaus Hollig},
	Chapter = {Finite Element Approximation with Splines},
	Editor = {G. Farin and J. Hoschek and M.S. Kim},
	Owner = {tustison},
	Pages = {283-307},
	Publisher = {Elsevier},
	Title = {Handbook of Computer Aided Geometric Design},
	Year = {2002}}

@book{Hollig2004,
	Author = {Klaus Hollig},
	Owner = {tustison},
	Publisher = {SIAM (Society for Industrial and Applied Mathematics)},
	Title = {Finite Element Methods with B-Splines},
	Year = {2004}}

@article{Hollig2003,
	Author = {Klaus Hollig and Ulrich Reif},
	Journal = {Computer Aided Geometric Design},
	Number = {20},
	Owner = {tustison},
	Pages = {277-294},
	Title = {Nonuniform Web-Splines},
	Year = {2003}}

@article{Hollig2001,
	Author = {Klaus Hollig and Ulrich Reif and Joachim Wipper},
	Journal = {Siam Journal of Numerical Analysis},
	Number = {2},
	Owner = {tustison},
	Pages = {442-462},
	Title = {Weighted Extended B-Spline Approximation of Dirichlet Problems},
	Volume = {39},
	Year = {2001}}

@article{Horn1981,
	Author = {B. Horn and B. Schunk},
	Journal = {Artificial Intelligence},
	Pages = {185-283},
	Timestamp = {2006.12.20},
	Title = {Determining Optical Flow},
	Volume = {17},
	Year = {1981}}

@article{Hospedales2008,
	Author = {Hospedales, Timothy M. and Vijayakumar, Sethu},
	Doi = {10.1109/TPAMI.2008.25},
	Journal = IEEE_J_PAMI,
	Month = {Dec.},
	Number = {12},
	Pages = {2140--2157},
	Timestamp = {2008.11.26},
	Title = {Structure Inference for Bayesian Multisensory Scene Understanding},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2008.25}}

@article{Hsu1992,
	Author = {W. M. Hsu and J. F. Hughes and H. Kaufman},
	Journal = {Computer Graphics},
	Pages = {177-184},
	Timestamp = {2007.08.01},
	Title = {Direct Manipulation of Free-Form Deformations},
	Volume = {26},
	Year = {1992}}

@article{Hu2001,
	Author = {Shiying Hu and Eric A. Hoffman and Joseph M. Reinhardt},
	Journal = {IEEE Transactions on Medical Imaging},
	Number = {6},
	Owner = {tustison},
	Pages = {490-498},
	Title = {Automatic Lung Segmentation for Accurate Quantitation of Volumetric X-Ray CT Images},
	Volume = {20},
	Year = {2001}}

@article{Hua2007,
	Author = {Hong Hua and Ahuja, N. and Chunyu Gao},
	Doi = {10.1109/TPAMI.2007.33},
	Journal = IEEE_J_PAMI,
	Month = {Feb.},
	Number = {2},
	Pages = {356--361},
	Timestamp = {2008.11.26},
	Title = {Design Analysis of a High-Resolution Panoramic Camera Using Conventional Imagers and a Mirror Pyramid},
	Volume = {29},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.33}}

@inproceedings{Ibanez2006,
	Author = {Luis Ibanez and Ricardo S. Avila and Stephen R. Aylward},
	Booktitle = {Proc. of the International Symposium on Biomedical Imaging},
	Timestamp = {2009.05.18},
	Title = {Open Source and Open Science: how it is changing the medical imaging community},
	Year = {2006}}

@inproceedings{Ibanez2002,
	Author = {Luis Ibanez and Lydia Ng and James C. Gee and Stephen Aylward},
	Booktitle = {IEEE International Symposium on Biomedical Imaging},
	Month = {July},
	Owner = {tustison},
	Pages = {345-348},
	Title = {Registration Patterns: The Generic Framework for Image Registration of the {I}nsight {T}oolkit},
	Year = {2002}}

@book{Ibanez2005,
	Author = {Luis Ibanez and Will Schroeder and Lydia Ng and Josh Cates},
	Edition = {2},
	Month = {November},
	Organization = {Insight Software Consortium},
	Publisher = {Kitware, Inc., Albany, NY},
	Timestamp = {2006.12.20},
	Title = {The ITK Software Guide},
	Year = {2005}}

@manual{Ibanez2005a,
	Author = {Luis Ibanez and Will Schroeder and Lydia Ng and Josh Cates},
	Edition = {2},
	Month = {November},
	Organization = {Insight Software Consortium},
	Timestamp = {2009.05.18},
	Title = {The ITK Software Guide},
	Year = {2005}}

@article{Iwasawa2007,
	Author = {Tae Iwasawa and Hiroshi Takahashi and Takashi Ogura and Akira Asakura and Toshiyuki Gotoh and Seiichiro Kagei and Jun-Ichi Nishimura and Makoto Obara and Tomio Inoue},
	Journal = {J Magn Reson Imaging},
	Month = {Dec},
	Number = {6},
	Pages = {1530--1536},
	Timestamp = {2009.05.18},
	Title = {Correlation of lung parenchymal {MR} signal intensity with pulmonary function tests and quantitative computed tomography (CT) evaluation: A pilot study.},
	Volume = {26},
	Year = {2007}}

@inproceedings{Jian2005,
	Author = {B. Jian and B. Vemuri},
	Booktitle = {Proceedings of the International Conference on Computer Vision},
	Pages = {1246-1251},
	Timestamp = {2008.09.04},
	Title = {A robust algorithm for point set registration using mixture of {Gaussians}},
	Year = {2005}}

@article{Johnson1998,
	Author = {J. L. Johnson and S. S. Kramer and S. Mahboubi},
	Journal = {Radiology},
	Month = {Jan},
	Number = {1},
	Pages = {95--101},
	Timestamp = {2009.05.18},
	Title = {Air trapping in children: evaluation with dynamic lung densitometry with spiral {CT}.},
	Volume = {206},
	Year = {1998}}

@article{Jonsson2004,
	Author = {Gudbjorn F. Jonsson and Stephen A. Vavasis},
	Journal = {Mathematics of Computation},
	Number = {249},
	Owner = {tustison},
	Pages = {221-262},
	Title = {Accurate Solution of Polynomial Equations Using Macaulay Resultant Matrices},
	Volume = {74},
	Year = {2004}}

@article{Joshi2000,
	Author = {Sarang C. Joshi and Michael I. Miller},
	Journal = {IEEE Transactions on Image Processing},
	Number = {8},
	Owner = {tustison},
	Pages = {1357-1370},
	Title = {Landmark Matching via Large Deformation Diffeomorphisms},
	Volume = {9},
	Year = {2000}}

@article{Jr.2003,
	Author = {C. R. Maurer Jr. and Qi Rensheng and V. Raghavan},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {2},
	Owner = {tustison},
	Pages = {265-270},
	Title = {A linear time algorithm for computing exact Euclidean distance transforms of binary images in arbitrary dimensions},
	Volume = {25},
	Year = {2003}}

@article{Jupp1978,
	Author = {David L. B. Jupp},
	Journal = {SIAM Journal on Numerical Analysis},
	Number = {2},
	Owner = {tustison},
	Pages = {328-343},
	Title = {Approximation to Data by Splines with Free Knots},
	Volume = {15},
	Year = {1978}}

@inproceedings{Kadir2005,
	Author = {Timor Kadir and Michael Brady},
	Booktitle = {British Machine Vision Conference},
	Owner = {tustison},
	Title = {Estimating statistics in arbitrary regions of interest},
	Year = {2005}}

@article{Kagan1998,
	Author = {Pavel Kagan and Anath Fischer and Pinhas Z. Bar-Yoseph},
	Journal = {International Journal for Numerical Methods in Engineering},
	Owner = {tustison},
	Pages = {435-458},
	Title = {New B-Spline Finite Element Approach for Geometric Design and Mechanical Analysis},
	Volume = {41},
	Year = {1998}}

@article{Kalender1990,
	Author = {W. A. Kalender and W. Seissler and E. Klotz and P. Vock},
	Journal = {Radiology},
	Month = {Jul},
	Number = {1},
	Pages = {181--183},
	Timestamp = {2009.05.18},
	Title = {Spiral volumetric {CT} with single-breath-hold technique, continuous transport, and continuous scanner rotation.},
	Volume = {176},
	Year = {1990}}

@article{Kauczor1998,
	Author = {H. U. Kauczor and C. P. Heussel and B. Fischer and R. Klamm and P. Mildenberger and M. Thelen},
	Journal = {AJR Am J Roentgenol},
	Month = {Oct},
	Number = {4},
	Pages = {1091--1095},
	Timestamp = {2009.05.18},
	Title = {Assessment of lung volumes using helical {CT} at inspiration and expiration: comparison with pulmonary function tests.},
	Volume = {171},
	Year = {1998}}

@article{Kauczor2002,
	Author = {Hans-Ulrich Kauczor and Jochem Hast and Claus Peter Heussel and Jens Schlegel and Peter Mildenberger and Manfred Thelen},
	Journal = {Eur Radiol},
	Month = {Nov},
	Number = {11},
	Pages = {2757--2763},
	Timestamp = {2009.05.18},
	Title = {{CT} attenuation of paired HRCT scans obtained at full inspiratory/expiratory position: comparison with pulmonary function tests.},
	Volume = {12},
	Year = {2002}}

@article{Kenney2003,
	Author = {Kenney, C.S. and Manjunath, B.S. and Zuliani, M. and Hewer, G.A. and Van Nevel, A.},
	Doi = {10.1109/TPAMI.2003.1240118},
	Journal = IEEE_J_PAMI,
	Month = {Nov.},
	Number = {11},
	Pages = {1437--1454},
	Timestamp = {2008.11.26},
	Title = {A condition number for point matching with application to registration and postregistration error estimation},
	Volume = {25},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2003.1240118}}

@article{Kesten1993,
	Abstract = {To assess awareness and understanding of obstructive airway diseases by primary-care physicians, the authors surveyed a randomly selected population of 75 primary care practitioners. During one-on-one interviews, physicians were presented with a standardized case scenario and a subsequent series of open-ended questions concerning asthma and COPD. Each respondent was presented in randomized fashion with one of two versions of a case description of a hypothetical 52-year-old male smoker with a recent upper respiratory tract infection and persistent productive cough. The only difference between case descriptions was that one included explicit reference to an earlier tentative diagnosis of chronic bronchitis (CB version); the other description made no specific mention of this diagnostic term (NCB version). Chest radiographs were requested by 80 percent of physicians and sputum cultures by 50 percent, these percentages not differing significantly between CB and NCB groups. Spirometry was requested less often than either of the foregoing tests (21 percent). The CB group requested spirometry significantly more often than the NCB group (38 percent vs 5 percent, p < 0.05). The most frequently mentioned primary diagnosis was bronchitis/pneumonia (33 percent), followed by bronchitis (28 percent) and chronic bronchitis (16 percent), all of which were similar in both groups. However, the diagnostic term "COPD" was the primary diagnosis in 16 percent of the CB group, compared with 8 percent in the NCB group (p > 0.05). Oral antibiotics were the most frequently chosen first-line drug therapy (63 percent). In subsequent questions concerning the management of obstructive airway diseases, primary practitioners distinguished COPD from asthma conceptually, but their prescribed therapy for the two disorders was less distinct. beta 2-agonists were selected most frequently and similarly as initial therapy for both disorders (53 percent). Minor differences between first-line therapeutic choices included nonsignificant trends toward the more frequent mention of anticholinergic bronchodilators for COPD than for asthma (10 percent vs 0 percent) and the more frequent selection of inhaled corticosteroids for asthma (12 percent vs 5 percent). The authors conclude that to the extent that questionnaire responses reflect actual practice, primary care practitioners (1) have a low index of suspicion for obstructive airway disease, (2) markedly underutilized spirometry as a screening tool, (3) consider beta 2-agonists first-line therapy for COPD and asthma, and (4) despite considering COPD and asthma different disease processes, choose similar medications for each disorder.},
	Author = {S. Kesten and K. R. Chapman},
	Institution = {Asthma Centre, Toronto Hospital, Ontario, Canada.},
	Journal = {Chest},
	Keywords = {Airway Obstruction; Anti-Bacterial Agents; Asthma; Attitude of Health Personnel; Bronchitis; Bronchodilator Agents; Chronic Disease; Cough; Emphysema; Humans; Life Style; Lung Diseases, Obstructive; Male; Middle Aged; Physicians, Family; Respiratory Function Tests; Respiratory Tract Infections; Smoking; Sputum},
	Month = {Jul},
	Number = {1},
	Pages = {254--258},
	Pmid = {8325079},
	Timestamp = {2009.05.18},
	Title = {Physician perceptions and management of COPD.},
	Volume = {104},
	Year = {1993}}

@article{Kim2008,
	Author = {Junghoon Kim and Brian Avants and Sunil Patel and John Whyte and Branch H Coslett and John Pluta and John A Detre and James C Gee},
	Journal = {Neuroimage},
	Month = {Feb},
	Number = {3},
	Pages = {1014--1026},
	Timestamp = {2009.05.18},
	Title = {Structural consequences of diffuse traumatic brain injury: a large deformation tensor-based morphometry study.},
	Volume = {39},
	Year = {2008}}

@article{Kim2008a,
	Author = {Kim, Jonghwa and Andr\& Elisabeth},
	Doi = {10.1109/TPAMI.2008.26},
	Journal = IEEE_J_PAMI,
	Month = {Dec.},
	Number = {12},
	Pages = {2067--2083},
	Timestamp = {2008.11.26},
	Title = {Emotion Recognition Based on Physiological Changes in Music Listening},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2008.26}}

@article{King2000,
	Journal = {Am J Respir Crit Care Med},
	Month = {Feb},
	Number = {2 Pt 1},
	Pages = {574--580},
	Timestamp = {2009.05.18},
	Title = {An analysis algorithm for measuring airway lumen and wall areas from high-resolution computed tomographic data.},
	Volume = {161},
	Year = {2000}}

@article{Kinsella1990,
	Journal = {Chest},
	Month = {Feb},
	Number = {2},
	Pages = {315--321},
	Timestamp = {2009.05.18},
	Title = {Quantitation of emphysema by computed tomography using a "density mask" program and correlation with pulmonary function tests.},
	Volume = {97},
	Year = {1990}}

@article{Kiryu2008,
	Author = {Shigeru Kiryu and Tessa Sundaram and Shigeto Kubo and Kuni Ohtomo and Toshio Asakura and James C Gee and Hiroto Hatabu and Masaya Takahashi},
	Journal = {J Magn Reson Imaging},
	Month = {Jan},
	Number = {1},
	Pages = {49--56},
	Timestamp = {2009.05.18},
	Title = {{MRI} assessment of lung parenchymal motion in normal mice and transgenic mice with sickle cell disease.},
	Volume = {27},
	Year = {2008}}

@inproceedings{Kiryu2003,
	Author = {S. Kiryu and M. Takahashi and T.A. Sundaram and J.C. Gee and Y. Mori and H. Uematsu and T. Asakura and H. Hatabu},
	Booktitle = {Proc. of the 11th Annual Meeting of ISMRM},
	Timestamp = {2009.05.18},
	Title = {Magnetic Resonance Lung Deformation Map of Normal Mice and Transgenic Mice Model of Sickle Cell Disease},
	Year = {2003}}

@article{Kishi2002,
	Author = {K. Kishi and J. W. Gurney and D. R. Schroeder and P. D. Scanlon and S. J. Swensen and J. R. Jett},
	Journal = {Eur Respir J},
	Month = {Jun},
	Number = {6},
	Pages = {1093--1098},
	Timestamp = {2009.05.18},
	Title = {The correlation of emphysema or airway obstruction with the risk of lung cancer: a matched case-controlled study.},
	Volume = {19},
	Year = {2002}}

@article{Klassen2004,
	Author = {Eric Klassen and Anuj Srivastava and Washington Mio and Shantanu H. Joshi},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {3},
	Owner = {tustison},
	Pages = {372-383},
	Title = {Analysis of Planar Shapes Using Geodesic Paths on Shape Spaces},
	Volume = {26},
	Year = {2004}}

@article{Klein2009,
	Abstract = {All fields of neuroscience that employ brain imaging need to communicate their results with reference to anatomical regions. In particular, comparative morphometry and group analysis of functional and physiological data require coregistration of brains to establish correspondences across brain structures. It is well established that linear registration of one brain to another is inadequate for aligning brain structures, so numerous algorithms have emerged to nonlinearly register brains to one another. This study is the largest evaluation of nonlinear deformation algorithms applied to brain image registration ever conducted. Fourteen algorithms from laboratories around the world are evaluated using 8 different error measures. More than 45,000 registrations between 80 manually labeled brains were performed by algorithms including: AIR, ANIMAL, ART, Diffeomorphic Demons, FNIRT, IRTK, JRD-fluid, ROMEO, SICLE, SyN, and four different SPM5 algorithms ("SPM2-type" and regular Normalization, Unified Segmentation, and the DARTEL Toolbox). All of these registrations were preceded by linear registration between the same image pairs using FLIRT. One of the most significant findings of this study is that the relative performances of the registration methods under comparison appear to be little affected by the choice of subject population, labeling protocol, and type of overlap measure. This is important because it suggests that the findings are generalizable to new subject populations that are labeled or evaluated using different labeling protocols. Furthermore, we ranked the 14 methods according to three completely independent analyses (permutation tests, one-way ANOVA tests, and indifference-zone ranking) and derived three almost identical top rankings of the methods. ART, SyN, IRTK, and SPM's DARTEL Toolbox gave the best results according to overlap and distance measures, with ART and SyN delivering the most consistently high accuracy across subjects and label sets. Updates will be published on the http://www.mindboggle.info/papers/ website.},
	Author = {Arno Klein and Jesper Andersson and Babak A Ardekani and John Ashburner and Brian Avants and Ming-Chang Chiang and Gary E Christensen and Louis D Collins and James Gee and Pierre Hellier and Joo Hyun Song and Mark Jenkinson and Claude Lepage and Daniel Rueckert and Paul Thompson and Tom Vercauteren and Roger P Woods and J. John Mann and Ramin V Parsey},
	Doi = {10.1016/j.neuroimage.2008.12.037},
	Institution = {New York State Psychiatric Institute, Columbia University, NY, NY 10032, USA.},
	Journal = {Neuroimage},
	Month = {Jan},
	Pii = {S1053-8119(08)01297-4},
	Pmid = {19195496},
	Timestamp = {2009.03.03},
	Title = {Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration.},
	Url = {http://dx.doi.org/10.1016/j.neuroimage.2008.12.037},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuroimage.2008.12.037}}

@article{Klein1997,
	Author = {Andreas K. Klein and Forester Lee and Amir A. Amini},
	Journal = {IEEE Transactions on Medical Imaging},
	Number = {5},
	Owner = {tustison},
	Pages = {469-482},
	Title = {Quantitative Coronary Angiography with Deformable Spline Models},
	Volume = {16},
	Year = {1997}}

@misc{Klein,
	Author = {Stefan Klein and Marius Staring},
	Timestamp = {2006.06.19},
	Url = {http://www.isi.uu.nl/Elastix/},
	Bdsk-Url-1 = {http://www.isi.uu.nl/Elastix/}}

@article{Klein2007,
	Author = {Stefan Klein and Marius Staring and Josien P.W. Pluim},
	Journal = {IEEE Transactions on Image Processing},
	Month = {December},
	Number = {12},
	Pages = {2879-2890},
	Timestamp = {2008.10.02},
	Title = {Evaluation of Optimization Methods for Nonrigid Medical Image Registration using Mutual Information and B-splines},
	Volume = {16},
	Year = {2007}}

@article{Kolmogorov2004,
	Author = {Vladimir Kolmogorov and Ramin Zabih},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {2},
	Owner = {tustison},
	Pages = {147-159},
	Title = {What Energy Functions Can Be Minimized via Graph Cuts?},
	Volume = {26},
	Year = {2004}}

@article{Koumellis2005,
	Abstract = {PURPOSE: To investigate regional airways obstruction in patients with cystic fibrosis (CF) with quantitative analysis of dynamic hyperpolarized (HP) (3)He MRI. MATERIALS AND METHODS: Dynamic radial projection MRI of HP (3)He gas was used to study respiratory dynamics in a group of eight children with CF. Signal kinetics in a total of seven regions of interest (ROIs; three in each lung, and one in the trachea) were compared with the results of spirometric pulmonary function tests (PFTs). The tracheal signal intensity was used as a form of "input function" to normalize for input flow effects. RESULTS: A pattern of low flow rate in the upper lobes was observed. When the flow measurements from the peripheral ROIs were averaged to obtain an index of flow in the peripheral lung, a good correlation was found (P = 3.74 x 10(-5)) with the forced expired volume in one second (FEV1). CONCLUSION: These results suggest that a quantitative measurement of localized airways obstruction in the early stages of CF may be obtained from dynamic (3)He MRI by using the slope of the signal rise as a measure of air flow into the peripheral lung. This study also demonstrates that children can cooperate well with the (3)He MRI technique.},
	Author = {Panos Koumellis and Edwin J R van Beek and Neil Woodhouse and Stan Fichele and Andrew J Swift and Martyn N J Paley and Catherine Hill and Chris J Taylor and Jim M Wild},
	Doi = {10.1002/jmri.20402},
	Journal = {J Magn Reson Imaging},
	Keywords = {Adolescent; Airway Obstruction; Child; Cystic Fibrosis; Female; Humans; Magnetic Resonance Imaging; Male; Spirometry; Tritium},
	Month = {Sep},
	Number = {3},
	Pages = {420--426},
	Pmid = {16104046},
	Timestamp = {2007.06.06},
	Title = {Quantitative analysis of regional airways obstruction using dynamic hyperpolarized 3He MRI-preliminary results in children with cystic fibrosis.},
	Url = {http://dx.doi.org/10.1002/jmri.20402},
	Volume = {22},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/jmri.20402}}

@article{Kovacevic2006,
	Author = {Jelena Kovacevic},
	Journal = {IEEE Transactions on Image Processing},
	Month = {December},
	Number = {12},
	Pages = {3625-3626},
	Timestamp = {2007.08.03},
	Title = {From the Editor-in-Chief},
	Volume = {15},
	Year = {2006}}

@article{Kovacevic2006a,
	Author = {Jelena Kovacevic},
	Journal = {IEEE Transactions on Image Processing},
	Pages = {12},
	Timestamp = {2009.05.18},
	Title = {From the Editor-in-Chief},
	Volume = {15},
	Year = {2006}}

@article{Kriegman2008,
	Author = {Kriegman, David J. and Fleet, David and Ghahraman, Zoubin},
	Doi = {10.1109/TPAMI.2008.252},
	Journal = IEEE_J_PAMI,
	Month = {Dec.},
	Number = {12},
	Pages = {2065--2066},
	Timestamp = {2008.11.26},
	Title = {Introduction of New Associate Editors},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2008.252}}

@inproceedings{Krissian2003,
	Author = {K. Krissian and C. F. Westin},
	Booktitle = {EUROCAST NeuroImaging Workshop},
	Month = {February},
	Organization = {Ninth International Conference on Computer Aided Systems Theory},
	Owner = {tustison},
	Pages = {48-51},
	Title = {Fast and Accurate Redistancing for Level Set Methods},
	Year = {2003}}

@inproceedings{Kubo2007,
	Author = {S. Kubo and T.A. Sundaram and J.C. Gee and H. Hatabu and M. Takahashi},
	Booktitle = {Proc. of the 15th Annual Meeting of ISMRM},
	Pages = {2779},
	Timestamp = {2009.05.18},
	Title = {Four-dimensional volumetric analysis of the lung over the respiratory cycle in ventilated mice with emphysema},
	Year = {2007}}

@inproceedings{Kubo2006,
	Author = {S. Kubo and T.A. Sundaram and J.C. Gee and H. Hatabu and M. Takahashi},
	Booktitle = {Proc. of the 14th Annual Meeting of ISMRM},
	Pages = {40},
	Timestamp = {2009.05.18},
	Title = {Three-dimensional volumetric analysis of the lung during respiration in ventilated mice},
	Year = {2006}}

@inproceedings{Kubo2006a,
	Author = {S. Kubo and T.A. Sundaram and S. Kiryu and Y. Mori and J.C. Gee and H. Hatabu and M. Takahashi},
	Booktitle = {Proc. of the 14th Annual Meeting of ISMRM},
	Timestamp = {2009.05.18},
	Title = {Voxel-wise analysis of lung parenchymal motion during breathing via a non-rigid registration algorithm in human: dynamic {MRI} in different postures},
	Year = {2006}}

@article{Kuijpers2003,
	Abstract = {BACKGROUND: The purpose of this study was to assess the value of high-dose dobutamine cardiovascular magnetic resonance (CMR) with myocardial tagging for the detection of wall motion abnormalities as a measure of myocardial ischemia in patients with known or suspected coronary artery disease. METHODS AND RESULTS: Two hundred eleven consecutive patients with chest pain underwent dobutamine-CMR 4 days after antianginal medication was stopped. Dobutamine-CMR was performed at rest and during increasing doses of dobutamine. Cine-images were acquired during breath-hold with and without myocardial tagging at 3 short-axis levels. Regional wall motion was assessed in a 16-segment short-axis model. Patients with new wall motion abnormalities (NWMA) were examined by coronary angiography. Dobutamine-CMR was successfully performed in 194 patients. Dobutamine-CMR without tagging detected NWMA in 58 patients, whereas NWMA were detected in 68 patients with tagging (P=0.002, McNemar). Coronary angiography showed coronary artery disease in 65 (96\%) of these 68 patients. All but 3 of the 65 patients needed revascularization. In the 112 patients with a negative dobutamine-CMR study, without baseline wall motion abnormalities, the cardiovascular occurrence-free survival rate was 98.2\% during the mean follow-up period of 17.3 months (range, 7 to 31). CONCLUSIONS: Dobutamine-CMR with myocardial tagging detected more NWMA compared with dobutamine-CMR without tagging and reliably separated patients with a normal life expectancy from those at increased risk of major adverse cardiac events.},
	Author = {Dirkjan Kuijpers and Kai Yiu J A M Ho and Paul R M van Dijkman and Rozemarijn Vliegenthart and Matthijs Oudkerk},
	Doi = {10.1161/01.CIR.0000060544.41744.7C},
	Journal = {Circulation},
	Keywords = {Coronary Angiography; Disease-Free Survival; Dobutamine; Female; Heart; Humans; Magnetic Resonance Imaging; Male; Middle Aged; Motion; Myocardial Ischemia; Survival Rate},
	Month = {Apr},
	Number = {12},
	Pages = {1592--1597},
	Pii = {01.CIR.0000060544.41744.7C},
	Pmid = {12668491},
	Timestamp = {2007.09.09},
	Title = {Dobutamine cardiovascular magnetic resonance for the detection of myocardial ischemia with the use of myocardial tagging.},
	Url = {http://dx.doi.org/10.1161/01.CIR.0000060544.41744.7C},
	Volume = {107},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1161/01.CIR.0000060544.41744.7C}}

@article{Lamers1998,
	Author = {R. J. Lamers and G. J. Kemerink and M. Drent and J. M. van Engelshoven},
	Journal = {Eur Respir J},
	Month = {Apr},
	Number = {4},
	Pages = {942--945},
	Timestamp = {2009.05.18},
	Title = {Reproducibility of spirometrically controlled {CT} lung densitometry in a clinical setting.},
	Volume = {11},
	Year = {1998}}

@article{Lamers1994,
	Author = {R. J. Lamers and G. R. Thelissen and A. G. Kessels and E. F. Wouters and J. M. van Engelshoven},
	Journal = {Radiology},
	Month = {Oct},
	Number = {1},
	Pages = {109--113},
	Timestamp = {2009.05.18},
	Title = {Chronic obstructive pulmonary disease: evaluation with spirometrically controlled {CT} lung densitometry.},
	Volume = {193},
	Year = {1994}}

@article{Lamousin1994,
	Author = {Henry J. Lamousin and Warren N. Waggenspack Jr.},
	Journal = {IEEE Computer Graphics and Applications},
	Number = {6},
	Owner = {tustison},
	Pages = {59-65},
	Title = {NURBS-Based Free-Form Deformations},
	Volume = {14},
	Year = {1994}}

@article{Lange2006,
	Abstract = {BACKGROUND: Accurate characterization of asthma severity is difficult due to the variability of symptoms. Hyperpolarized helium-3 MRI (H(3)HeMR) is a new technique in which the airspaces are visualized, depicting regions with airflow obstruction as "ventilation defects." The objective of this study was to compare the extent of H(3)HeMR ventilation defects with measures of asthma severity and spirometry. METHODS: Patients with a physician diagnosis of asthma and normal control subjects underwent H(3)HeMR. For each person, the number and size of ventilation defects were scored and the average number of ventilation defects per slice (VDS) was calculated. The correlations of the imaging findings with measures of asthma severity and spirometry were determined. RESULTS: There were 58 patients with asthma (mild-intermittent, n = 13; mild-persistent, n = 13; moderate-persistent, n = 20; and severe-persistent, n = 12) and 18 control subjects. Mean +/- SE VDS for asthmatics was significantly greater than for control subjects (0.99 +/- 0.15 vs 0.26 +/- 0.22, p = 0.004). Among asthmatics, VDS was significantly higher for the group with moderate-persistent and severe-persistent disease than for the group with mild-intermittent and mild-persistent disease (1.37 +/- 0.24 vs 0.53 +/- 0.12, p < 0.001). VDS correlated significantly with FEV(1)/FVC (r = - 0.51, p = 0.002), forced expiratory flow between 25\% and 75\% from the beginning of FVC (FEF(25-75\%)) percentage of predicted for height, sex, and race (\%predicted) [r = - 0.50, p = 0.001], and FEV(1) \%predicted (r = - 0.40, p = 0.002), but not with FVC \%predicted (r = - 0.26, p = 0.057) and peak expiratory flow \%predicted (r = - 0.16, p = 0.231). Many asthmatics had an elevated VDS, but their spirometric indexes, except FEF(25\%-75\%), were normal. Most ventilation defects were < 3 cm in size for all asthmatics. In the group of patients with moderate-to-severe persistent asthma, there were more defects > or =3 cm than in the group with mild-intermittent and mild-persistent disease (p = 0.021). CONCLUSIONS: Regional changes of airflow obstruction in asthmatics depicted by H(3)HeMR correlate with measures of asthma severity and spirometry.},
	Author = {Eduard E de Lange and Talissa A Altes and James T Patrie and John D Gaare and Jeffrey J Knake and John P Mugler and Thomas A Platts-Mills},
	Doi = {10.1378/chest.130.4.1055},
	Journal = {Chest},
	Keywords = {Adolescent; Adult; Airway Obstruction; Asthma; Forced Expiratory Volume; Hel; Humans; Image Enhancement; Image Processing, Computer-Assisted; Isotopes; Lung; Magnetic Resonance Imaging; Male; Maximal Midexpiratory Flow Rate; Spirometry; Statistics; Vital Capacity; ium},
	Month = {Oct},
	Number = {4},
	Pages = {1055--1062},
	Pii = {130/4/1055},
	Pmid = {17035438},
	Timestamp = {2007.06.06},
	Title = {Evaluation of asthma with hyperpolarized helium-3 MRI: correlation with clinical severity and spirometry.},
	Url = {http://dx.doi.org/10.1378/chest.130.4.1055},
	Volume = {130},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1378/chest.130.4.1055}}

@article{Lange2007,
	Abstract = {BACKGROUND: It is unknown whether focal changes of airflow obstruction within the lungs of patients with asthma vary or are fixed in location with time or repeated bronchoconstriction. With hyperpolarized helium-3 magnetic resonance (H(3)HeMR) imaging, the airspaces are depicted and focal areas of airflow obstruction are shown as "ventilation defects." OBJECTIVE: To investigate the regional changes of airflow obstruction with time and repeated bronchoconstriction. METHODS: H(3)HeMR and spirometry were performed before (pre) and immediately after (post) methacholine challenge in 10 young patients with asthma on 2 days that were 7-476 days (mean, 185.3 +/- 37.2 days) apart. Pair-wise image comparisons were performed to determine the change in location of ventilation defects within the lung and their change in size. RESULTS: When comparing premethacholine versus premethacholine and postmethacholine versus post-methacholine images of the 2 days, 41\% +/- 10\% and 69\% +/- 5\% (P = .017) of defects, respectively, were in the same location, and of those, 69\% +/- 12\% and 43\% +/- 5\% (P = .022), respectively, did not change size. Comparing premethacholine versus postmethacholine images, 58\% +/- 9\% of defects were in the same location on day 1 and 73\% +/- 7\% (P = .088) on day 2. On both days, the percent increase in defect number from premethacholine to postmethacholine was much greater than the percent decrease in spirometric values (P < .001). CONCLUSION: Many of the ventilation defects persisted or recurred in the same location with time or repeated bronchoconstriction, suggesting that the regional changes of airflow obstruction are relatively fixed within the lung. CLINICAL IMPLICATIONS: The findings give new insight into the regional airflow variability within the lungs of patients with asthma.},
	Author = {Eduard E de Lange and Talissa A Altes and James T Patrie and Jaywant Parmar and James R Brookeman and John P Mugler and Thomas A E Platts-Mills},
	Doi = {10.1016/j.jaci.2006.12.659},
	Institution = {Department of Radiology, University of Virginia, Charlottesville, VA 22908, USA. delange@virginia.edu},
	Journal = {J Allergy Clin Immunol},
	Keywords = {Adult; Airway Obstruction; Asthma; Bronchial Provocation Tests; Bronchoconstrictor Agents; Female; Helium; Humans; Lung; Magnetic Resonance Imaging; Methacholine Chloride; Middle Aged; Radioisotopes; Radiopharmaceuticals; Spirometry},
	Month = {May},
	Number = {5},
	Pages = {1072--1078},
	Pii = {S0091-6749(07)00161-3},
	Pmid = {17353032},
	Timestamp = {2008.01.10},
	Title = {The variability of regional airflow obstruction within the lungs of patients with asthma: assessment with hyperpolarized helium-3 magnetic resonance imaging.},
	Url = {http://dx.doi.org/10.1016/j.jaci.2006.12.659},
	Volume = {119},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.jaci.2006.12.659}}

@article{Lange1999,
	Abstract = {Thirty-two magnetic resonance imaging examinations of the lungs were performed in 16 subjects after inhalation of 1-2 L of helium 3 gas that was laser polarized to 10\%-25\%. The distribution of the gas was generally uniform, with visualization of the fissures in most cases. Ventilation defects were demonstrated in smokers and in a subject with allergies. The technique has potential for evaluating small airways disease.},
	Author = {E. E. de Lange and J. P. Mugler and J. R. Brookeman and J. Knight-Scott and J. D. Truwit and C. D. Teates and T. M. Daniel and P. L. Bogorad and G. D. Cates},
	Journal = {Radiology},
	Keywords = {Admi; Adult; Aged; Asthma; Female; Helium; Humans; Image Processing, Computer-Assisted; Isotopes; Lasers; Lung; Magnetic Resonance Imaging; Male; Middle Aged; Observer Variation; Oxygen; Pulmonary Emphysema; Respiration; Rhinitis, Allergic, Seasonal; Smoking; nistration, Inhalation},
	Month = {Mar},
	Number = {3},
	Pages = {851--857},
	Pmid = {10207491},
	Timestamp = {2007.06.06},
	Title = {Lung air spaces: {MR} imaging evaluation with hyperpolarized {3He} gas.},
	Volume = {210},
	Year = {1999}}

@article{Latecki95,
	Author = {Longin Latecki and Ulrich Eckhardt and Azriel Rosenfeld},
	Journal = {Computer Vision and Image Understanding},
	Pages = {70-83},
	Title = {Well-Composed Sets},
	Volume = {61},
	Year = {1995}}

@article{Laurent-Gengoux1993,
	Author = {Pascal Laurent-Gengoux and Mounib Mekhilef},
	Journal = {Computer-Aided Design},
	Number = {11},
	Owner = {tustison},
	Pages = {699-710},
	Title = {Optimization of a NURBS representation},
	Volume = {25},
	Year = {1993}}

@article{Lee2009,
	Author = {Lee, Mun Wai and Nevatia, Ramakant},
	Doi = {10.1109/TPAMI.2008.35},
	Journal = IEEE_J_PAMI,
	Month = {Jan.},
	Number = {1},
	Pages = {27--38},
	Timestamp = {2008.11.26},
	Title = {Human Pose Tracking in Monocular Sequence Using Multilevel Structured Models},
	Volume = {31},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2008.35}}

@article{Lee1997,
	Author = {Seungyong Lee and George Wolberg and Sung Yong Shin},
	Journal = {IEEE Transactions on Visualization and Computer Graphics},
	Number = {3},
	Owner = {tustison},
	Pages = {228-244},
	Title = {Scattered Data Interpolation with Multilevel B-Splines},
	Volume = {3},
	Year = {1997}}

@article{Leemput1999,
	Abstract = {We propose a model-based method for fully automated bias field correction of MR brain images. The MR signal is modeled as a realization of a random process with a parametric probability distribution that is corrupted by a smooth polynomial inhomogeneity or bias field. The method we propose applies an iterative expectation-maximization (EM) strategy that interleaves pixel classification with estimation of class distribution and bias field parameters, improving the likelihood of the model parameters at each iteration. The algorithm, which can handle multichannel data and slice-by-slice constant intensity offsets, is initialized with information from a digital brain atlas about the a priori expected location of tissue classes. This allows full automation of the method without need for user interaction, yielding more objective and reproducible results. We have validated the bias correction algorithm on simulated data and we illustrate its performance on various MR images with important field inhomogeneities. We also relate the proposed algorithm to other bias correction algorithms.},
	Author = {K Van Leemput and F Maes and D Vandermeulen and P Suetens},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Algorithms, Brain, Comparative Study, Computer Simulation, Humans, Image Enhancement, Imaging, Three-Dimensional, Likelihood Functions, Magnetic Resonance Imaging, Models, Biological, Models, Statistical, Pattern Recognition, Automated, Phantoms, Imaging, Quality Control, Reproducibility of Results, Research Support, Non-U.S. Gov't, Sensitivity and Specificity, Algorithms, Brain, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Multiple Sclerosis, Research Support, Non-U.S. Gov't, Algorithms, Bias (Epidemiology), Brain, Comparative Study, Computer Simulation, Humans, Likelihood Functions, Magnetic Resonance Imaging, Markov Chains, Models, Neurological, Reproducibility of Results, Research Support, Non-U.S. Gov't, Algorithms, Bias (Epidemiology), Brain, Comparative Study, Humans, Magnetic Resonance Imaging, Models, Neurological, Reproducibility of Results, Research Support, Non-U.S. Gov't, Schizophrenia, 10628948},
	Month = {Oct},
	Number = {10},
	Owner = {tustison},
	Pages = {885-96},
	Title = {Automated model-based bias field correction of {MR} images of the brain.},
	Volume = {18},
	Year = {1999}}

@article{Lehmann1999,
	Author = {Thomas M. Lehmann and Claudia Gonner},
	Journal = {IEEE Transactions on Medical Imaging},
	Owner = {tustison},
	Title = {Survey: Interpolation Methods in Medical Image Processing},
	Volume = {18},
	Year = {1999}}

@article{Lehmann2001,
	Author = {Thomas M. Lehmann and Claudia Gonner and Klaus Spitzer},
	Journal = {IEEE Transactions on Medical Imaging},
	Number = {7},
	Owner = {tustison},
	Pages = {660-665},
	Title = {Addendum: B-Spline Interpolation in Medical Image Processing},
	Volume = {20},
	Year = {2001}}

@article{Ley-Zaporozhan2007,
	Journal = {Eur J Radiol},
	Month = {May},
	Number = {2},
	Pages = {228--234},
	Timestamp = {2009.05.18},
	Title = {Quantitative analysis of emphysema in {3D} using {MDCT}: Influence of different reconstruction algorithms.},
	Volume = {65},
	Year = {2007}}

@inproceedings{Li2002,
	Author = {Baojun Li and Gary E. Christensen and John Dill and Eric A. Hoffman and Joseph M. Reinhardt},
	Booktitle = {Proceedings of SPIE: Medical Imaging},
	Owner = {tustison},
	Title = {3-{D} Inter-Subject Warping and Registration of Pulmonary {CT} Images for a Human Lung Models},
	Year = {2002}}

@article{Li2003a,
	Author = {Baojun Li and Gary E Christensen and Eric A Hoffman and Geoffrey McLennan and Joseph M Reinhardt},
	Journal = {Acad Radiol},
	Month = {Mar},
	Number = {3},
	Pages = {255--265},
	Timestamp = {2009.05.18},
	Title = {Establishing a normative atlas of the human lung: intersubject warping and registration of volumetric {CT} images.},
	Volume = {10},
	Year = {2003}}

@inproceedings{Li2005,
	Author = {Kang Li and Steven Millington and Xiadodong Wu and Danny Z. Chen and Milan Sonka},
	Booktitle = {Information Processing in Medical Imaging},
	Owner = {tustison},
	Title = {Simultaneous Segmentation of Multiple Closed Surfaces Using Optimal Graph Searching},
	Year = {2005}}

@article{Li2003,
	Author = {Qiang Li and Shusuke Sone and Kunio Doi},
	Journal = {Medical Physics},
	Number = {8},
	Owner = {tustison},
	Pages = {2040-2051},
	Title = {Selective enhancement filters for nodules, vessels, and airway walls in two- and three-dimensional CT scans},
	Volume = {30},
	Year = {2003}}

@article{Li2000,
	Author = {Stan Z. Li},
	Journal = {Handbook of Statistics},
	Owner = {tustison},
	Pages = {1-43},
	Title = {Modeling Image Analysis Problems Using Markov Random Fields},
	Volume = {20},
	Year = {2000}}

@article{Li2004,
	Abstract = {Registration of multidate or multisensor images is an essential process in many image processing applications including remote sensing, medical image analysis, and computer vision. Control point (CP) and intensity are the two basic features used separately for image registration in the literature. In this paper, an exact maximum likelihood (EML) registration method, which combines both CP and intensity, is proposed for image alignment. The EML registration method maximizes the likelihood function based CP and intensity to estimate the registration parameters, including affine transformation and CP coordinates. The explicit formulas of the Cramer-Rao bound (CRB) are also derived for the proposed EML and conventional image registration algorithms. The performances of these image registration techniques are evaluated with the CRBs.},
	Author = {Winston Li and Henry Leung},
	Journal = {IEEE Trans Image Process},
	Keywords = {Algorithms, Comparative Study, Image Enhancement, Image Interpretation, Computer-Assisted, Likelihood Functions, Models, Statistical, Pattern Recognition, Automated, Reproducibility of Results, Sensitivity and Specificity, Signal Processing, Computer-Assisted, Subtraction Technique, 15326853},
	Month = {Aug},
	Number = {8},
	Owner = {tustison},
	Pages = {1115-27},
	Title = {A maximum likelihood approach for image registration using control point and intensity.},
	Volume = {13},
	Year = {2004}}

@article{Liao2004,
	Author = {Xuejun Liao and Carin, L.},
	Doi = {10.1109/TPAMI.2004.38},
	Journal = IEEE_J_PAMI,
	Month = {Aug.},
	Number = {8},
	Pages = {961--972},
	Timestamp = {2008.11.26},
	Title = {Application of the theory of optimal experiments to adaptive electromagnetic-induction sensing of buried targets},
	Volume = {26},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2004.38}}

@article{Lieshout2008,
	Author = {van Lieshout, M.N.M.},
	Doi = {10.1109/TPAMI.2008.45},
	Journal = IEEE_J_PAMI,
	Month = {July},
	Number = {7},
	Pages = {1308--1312},
	Timestamp = {2008.11.26},
	Title = {Depth Map Calculation for a Variable Number of Moving Objects using Markov Sequential Object Processes},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2008.45}}

@article{Lo1989,
	Author = {Chong-Huah Lo and Hon-Son Don},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {10},
	Owner = {tustison},
	Pages = {1053-1064},
	Title = {3-D Moment Forms: Their Construction and Application to Object Identification and Positioning},
	Volume = {11},
	Year = {1989}}

@article{Peng2005,
	Author = {Long,, Fuhui and Ding,, Chris},
	Journal = {IEEE Trans. Pattern Anal. Mach. Intell.},
	Number = {8},
	Pages = {1226--1238},
	Title = {Feature Selection Based on Mutual Information: Criteria of Max-Dependency, Max-Relevance, and Min-Redundancy},
	Volume = {27},
	Year = {2005}}

@article{Lorenson1987,
	Author = {William E. Lorenson and Harvey E. Cline},
	Journal = {Computer Graphics},
	Number = {4},
	Owner = {tustison},
	Pages = {163-169},
	Title = {Marching Cubes: A High Resolution 3D Surface Construction Algorithm},
	Volume = {21},
	Year = {1987}}

@article{Luo2002,
	Author = {Jiebo Luo and Etz, S.P. and Gray, R.T. and Singhal, A.},
	Doi = {10.1109/TPAMI.2002.1023811},
	Journal = IEEE_J_PAMI,
	Month = {Aug.},
	Number = {8},
	Pages = {1147--1151},
	Timestamp = {2008.11.26},
	Title = {Normalized Kemeny and Snell distance: a novel metric for quantitative evaluation of rank-order similarity of images},
	Volume = {24},
	Year = {2002},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2002.1023811}}

@article{Ma1995,
	Author = {Weiyin Ma and J. P. Kruth},
	Journal = {Computer-Aided Design},
	Pages = {663-675},
	Timestamp = {2006.04.12},
	Title = {Parameterization of randomly measured points for least squares fitting of B-spline curves and surfaces},
	Volume = {27},
	Year = {1995}}

@article{Madani2001,
	Author = {A. Madani and C. Keyzer and P. A. Gevenois},
	Journal = {Eur Respir J},
	Month = {Oct},
	Number = {4},
	Pages = {720--730},
	Timestamp = {2009.05.18},
	Title = {Quantitative computed tomography assessment of lung structure and function in pulmonary emphysema.},
	Volume = {18},
	Year = {2001}}

@article{Madani2007,
	Author = {Afarine Madani and Viviane De Maertelaer and Jacqueline Zanen and Pierre Alain Gevenois},
	Journal = {Radiology},
	Month = {Apr},
	Number = {1},
	Pages = {250--257},
	Timestamp = {2009.05.18},
	Title = {Pulmonary emphysema: radiation dose and section thickness at multidetector {CT} quantification--comparison with macroscopic and microscopic morphometry.},
	Volume = {243},
	Year = {2007}}

@article{Madani2006,
	Author = {Afarine Madani and Jacqueline Zanen and Viviane de Maertelaer and Pierre Alain Gevenois},
	Journal = {Radiology},
	Month = {Mar},
	Number = {3},
	Pages = {1036--1043},
	Timestamp = {2009.05.18},
	Title = {Pulmonary emphysema: objective quantification at multi-detector row {CT}--comparison with macroscopic and microscopic morphometry.},
	Volume = {238},
	Year = {2006}}

@article{Maes1999,
	Author = {Frederick Maes and Dirk Vandermeulen and Paul Suetens},
	Journal = {Medical Image Analysis},
	Number = {4},
	Owner = {tustison},
	Pages = {373-386},
	Title = {Comparative evaluation of multiresolution optimization strategies for multimodality image registration by maximization of mutual information},
	Volume = {3},
	Year = {1999}}

@article{Maintz1998,
	Abstract = {The purpose of this paper is to present a survey of recent (published in 1993 or later) publications concerning medical image registration techniques. These publications will be classified according to a model based on nine salient criteria, the main dichotomy of which is extrinsic versus intrinsic methods. The statistics of the classification show definite trends in the evolving registration techniques, which will be discussed. At this moment, the bulk of interesting intrinsic methods is based on either segmented points or surfaces, or on techniques endeavouring to use the full information content of the images involved.},
	Author = {JB Maintz and MA Viergever},
	Journal = {Med Image Anal},
	Keywords = {Abdomen, Diagnostic Imaging, Extremities, Head, Humans, Pelvis, Reproducibility of Results, Spine, Thorax, 10638851},
	Month = {Mar},
	Number = {1},
	Owner = {tustison},
	Pages = {1-36},
	Pii = {S1361841501800268},
	Title = {A survey of medical image registration.},
	Volume = {2},
	Year = {1998}}

@article{Majtey2004,
	Author = {A. Majtey and P. Lamberti and A. Plastino},
	Journal = {Physica A},
	Pages = {547-553},
	Timestamp = {2008.08.14},
	Title = {A monoparametric family of metrics for statistical mechanics},
	Volume = {344},
	Year = {2004}}

@article{Malladi1995,
	Author = {Ravikanth Malladi and James A. Sethian and Baba C. Vemuri},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {2},
	Owner = {tustison},
	Pages = {158-175},
	Title = {Shape Modeling with Front Propogation: A Level Set Approach},
	Volume = {17},
	Year = {1995}}

@article{Mao2003,
	Author = {Wenxin Mao and Linda H. Zhao},
	Journal = {Journal of the Royal Statistical Society: Series B},
	Number = {4},
	Owner = {tustison},
	Pages = {901-919},
	Title = {Free-knot polynomial splines with confidence intervals},
	Volume = {65},
	Year = {2003}}

@article{March2000,
	Author = {Riccardo March and Piero Barone},
	Journal = {SIAM Journal of Applied Mathematics},
	Number = {4},
	Owner = {tustison},
	Pages = {1137-1156},
	Title = {Reonstruction of a Piecewise Constant Function From Noisy Fourier Coefficients By Pade Method},
	Volume = {60},
	Year = {2000}}

@article{Marsh2007,
	Author = {Suzanne Marsh and Sarah Aldington and Mathew V Williams and Michael R Nowitz and Andrew Kingzett-Taylor and Mark Weatherall and Philippa M Shirtcliffe and Amanda A McNaughton and Alison Pritchard and Richard Beasley},
	Journal = {Respir Med},
	Month = {Jul},
	Number = {7},
	Pages = {1512--1520},
	Timestamp = {2009.05.18},
	Title = {Utility of lung density measurements in the diagnosis of emphysema.},
	Volume = {101},
	Year = {2007}}

@article{Marsland2004,
	Author = {Stephen Marsland and Carole J. Twining},
	Journal = {IEEE Transactions on Medical Imaging},
	Number = {8},
	Owner = {tustison},
	Pages = {1006-1020},
	Title = {Constructing Diffeomorphic Representations for the Groupwise Analysis of Nonrigid Registrations of Medical Images},
	Volume = {23},
	Year = {2004}}

@article{Martina2006,
	Author = {Martina, M. and Masera, G.},
	Doi = {10.1109/TPAMI.2006.59},
	Journal = IEEE_J_PAMI,
	Month = {March},
	Number = {3},
	Pages = {487--494},
	Timestamp = {2008.11.26},
	Title = {Mumford and Shah functional: VLSI analysis and implementation},
	Volume = {28},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2006.59}}

@article{Masood2000,
	Abstract = {Assessment of myocardial mechanics is an integral part of understanding and predicting heart disease. This review covers the two most common magnetic resonance (MR) methods used to measure myocardial motion: myocardial tagging and myocardial velocity mapping. Myocardial tagging has been well established in clinical research, despite its time-consuming postprocessing procedure. Myocardial velocity mapping uses the phase shifts of the spins to encode the velocity into the MR signal. This means that once the myocardial contours have been segmented, the data can be automatically processed to obtain quantitative measurements. Diffusion MR also has found applications in cardiac imaging, with preliminary results of myocardial fiber architecture being obtained recently. These three different MR techniques have provided valuable insights into the assessment of intrinsic cardiac mechanics. J. Magn. Reson. Imaging 2000;12:873-883.},
	Author = {S. Masood and G. Z. Yang and D. J. Pennell and D. N. Firmin},
	Journal = {J Magn Reson Imaging},
	Keywords = {Animals; Diastole; Humans; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Myocardial Contraction; Myocardial Infarction; Systole},
	Month = {Dec},
	Number = {6},
	Pages = {873--883},
	Pii = {3.0.CO;2-J},
	Pmid = {11105025},
	Timestamp = {2007.09.08},
	Title = {Investigating intrinsic myocardial mechanics: the role of MR tagging, velocity phase mapping, and diffusion imaging.},
	Volume = {12},
	Year = {2000}}

@article{Matsumoto2006,
	Author = {Sumiaki Matsumoto and Harold L Kundel and James C Gee and Warren B Gefter and Hiroto Hatabu},
	Journal = {Med Image Anal},
	Month = {Jun},
	Number = {3},
	Pages = {343--352},
	Timestamp = {2009.05.18},
	Title = {Pulmonary nodule detection in {CT} images with quantized convergence index filter.},
	Volume = {10},
	Year = {2006}}

@article{Matsuoka2007,
	Author = {Shin Matsuoka and Yasuyuki Kurihara and Kunihiro Yagihashi and Yasuo Nakajima},
	Journal = {Respiration},
	Number = {2},
	Pages = {136--141},
	Timestamp = {2009.05.18},
	Title = {Quantitative thin-section {CT} analysis of the enlargement and coalescence of low-attenuation clusters in patients with emphysema.},
	Volume = {74},
	Year = {2007}}

@article{Matsuoka2007a,
	Author = {Shin Matsuoka and Yasuyuki Kurihara and Kunihiro Yagihashi and Yasuo Nakajima},
	Journal = {J Comput Assist Tomogr},
	Number = {3},
	Pages = {384--389},
	Timestamp = {2009.05.18},
	Title = {Quantitative assessment of peripheral airway obstruction on paired expiratory/inspiratory thin-section computed tomography in chronic obstructive pulmonary disease with emphysema.},
	Volume = {31},
	Year = {2007}}

@article{Mattes2003,
	Abstract = {We have implemented and validated an algorithm for three-dimensional positron emission tomography transmission-to-computed tomography registration in the chest, using mutual information as a similarity criterion. Inherent differences in the two imaging protocols produce significant nonrigid motion between the two acquisitions. A rigid body deformation combined with localized cubic B-splines is used to capture this motion. The deformation is defined on a regular grid and is parameterized by potentially several thousand coefficients. Together with a spline-based continuous representation of images and Parzen histogram estimates, our deformation model allows closed-form expressions for the criterion and its gradient. A limited-memory quasi-Newton optimization algorithm is used in a hierarchical multiresolution framework to automatically align the images. To characterize the performance of the method, 27 scans from patients involved in routine lung cancer staging were used in a validation study. The registrations were assessed visually by two expert observers in specific anatomic locations using a split window validation technique. The visually reported errors are in the 0- to 6-mm range and the average computation time is 100 min on a moderate-performance workstation.},
	Author = {David Mattes and David R Haynor and Hubert Vesselle and Thomas K Lewellen and William Eubank},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Algorithms, Artifacts, Carcinoma, Non-Small-Cell Lung, Fluorodeoxyglucose F18, Humans, Lung Neoplasms, Motion, Radiography, Thoracic, Radiopharmaceuticals, Research Support, U.S. Gov't, P.H.S., Subtraction Technique, Thorax, Tomography, Emission-Computed, 12703765},
	Month = {Jan},
	Number = {1},
	Owner = {tustison},
	Pages = {120-8},
	Title = {P{ET}-{CT} image registration in the chest using free-form deformations.},
	Volume = {22},
	Year = {2003}}

@article{Maurer2003,
	Author = {Maurer, C.R., Jr. and Rensheng Qi and Raghavan, V.},
	Doi = {10.1109/TPAMI.2003.1177156},
	Journal = IEEE_J_PAMI,
	Month = {Feb.},
	Number = {2},
	Pages = {265--270},
	Timestamp = {2008.11.26},
	Title = {A linear time algorithm for computing exact Euclidean distance transforms of binary images in arbitrary dimensions},
	Volume = {25},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2003.1177156}}

@article{McInerney2002,
	Abstract = {We introduce a new approach to medical image analysis that combines deformable model methodologies with concepts from the field of artificial life. In particular, we propose "deformable organisms", autonomous agents whose task is the automatic segmentation, labeling, and quantitative analysis of anatomical structures in medical images. Analogous to natural organisms capable of voluntary movement, our artificial organisms possess deformable bodies with distributed sensors, as well as (rudimentary) brains with motor, perception, behavior, and cognition centers. Deformable organisms are perceptually aware of the image analysis process. Their behaviors, which manifest themselves in voluntary movement and alteration of body shape, are based upon sensed image features, pre-stored anatomical knowledge, and a deliberate cognitive plan. We demonstrate several prototype deformable organisms based on a multiscale axisymmetric body morphology, including a "corpus callosum worm" that can overcome noise, incomplete edges, considerable anatomical variation, and interference from collateral structures to segment and label the corpus callosum in 2D mid-sagittal MR brain images.},
	Author = {Tim McInerney and Ghassan Hamarneh and Martha Shenton and Demetri Terzopoulos},
	Journal = {Med Image Anal},
	Keywords = {Algorithms, Comparative Study, Corpus Callosum, Expert Systems, Humans, Image Interpretation, Computer-Assisted, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Models, Biological, Models, Statistical, Movement, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, P.H.S., Sensitivity and Specificity, 12270230},
	Month = {Sep},
	Number = {3},
	Owner = {tustison},
	Pages = {251-66},
	Pii = {S136184150200083X},
	Title = {Deformable organisms for automatic medical image analysis.},
	Volume = {6},
	Year = {2002}}

@article{McMahon2006,
	Abstract = {The purpose of this study was to compare hyperpolarized 3helium magnetic resonance imaging (3He MRI) of the lungs in adults with cystic fibrosis (CF) with high-resolution computed tomography (HRCT) and spirometry. Eight patients with stable CF prospectively underwent 3He MRI, HRCT, and spirometry within 1 week. Three-dimensional (3D) gradient-echo sequence was used during an 18-s breath-hold following inhalation of hyperpolarized 3He. Each lung was divided into six zones; 3He MRI was scored as percentage ventilation per lung zone. HRCT was scored using a modified Bhalla scoring system. Univariate (Spearman rank) and multivariate correlations were performed between 3He MRI, HRCT, and spirometry. Results are expressed as mean+/-SD (range). Spirometry is expressed as percent predicted. There were four men and four women, mean age = 31.9+/-9 (20-46). Mean forced expiratory volume in 1 s (FEV)1 = 52\%+/-29 (27-93). Mean 3He MRI score = 74\%+/-25 (55-100). Mean HRCT score = 48.8+/-24 (13.5-83). The correlation between 3He MRI and HRCT was strong (R = +/-0.89, p < 0.001). Bronchiectasis was the only independent predictor of 3He MRI; 3He MRI correlated better with FEV1 and forced vital capacity (FVC) (R = 0.86 and 0.93, p < 0.01, respectively) than HRCT (R = +/-0.72 and +/-0.81, p < 0.05, respectively). This study showed that 3He MRI correlates strongly with structural HRCT abnormalities and is a stronger correlate of spirometry than HRCT in CF.},
	Author = {Colm J McMahon and Jonathan D Dodd and Catherine Hill and Neil Woodhouse and Jim M Wild and Stan Fichele and Charles G Gallagher and Stephen J Skehan and Edwin J R van Beek and James B Masterson},
	Doi = {10.1007/s00330-006-0311-5},
	Journal = {Eur Radiol},
	Month = {Nov},
	Number = {11},
	Pages = {2483--2490},
	Pmid = {16871384},
	Timestamp = {2007.06.06},
	Title = {Hyperpolarized 3helium magnetic resonance ventilation imaging of the lung in cystic fibrosis: comparison with high resolution CT and spirometry.},
	Url = {http://dx.doi.org/10.1007/s00330-006-0311-5},
	Volume = {16},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/s00330-006-0311-5}}

@article{McNitt-Gray1997,
	Author = {M. F. McNitt-Gray and J. G. Goldin and T. D. Johnson and D. P. Tashkin and D. R. Aberle},
	Journal = {J Comput Assist Tomogr},
	Number = {6},
	Pages = {939--947},
	Timestamp = {2009.05.18},
	Title = {Development and testing of image-processing methods for the quantitative assessment of airway hyperresponsiveness from high-resolution {CT} images.},
	Volume = {21},
	Year = {1997}}

@article{McVeigh1996,
	Abstract = {Methods for the noninvasive measurement of three-dimensional myocardial motion with MRI have recently been developed using presaturation tagging and velocity-encoded phase maps. The quality of clinical cardiac MRI studies has also recently improved with the advent of breath-hold scanning. The combination of breath-hold imaging with tagging and velocity-encoding sequences has made the measurement of myocardial wall motion in patients a simple and reproducible exam. These methods make it possible to quantify the severity and extent of regional heart wall motion abnormalities both at rest and during stress. This article reviews the MRI techniques developed for these applications.},
	Author = {E. R. McVeigh},
	Journal = {Magn Reson Imaging},
	Keywords = {Fourier Analysis; Heart; Heart Diseases; Humans; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Myocardial Contraction; Signal Processing, Computer-Assisted},
	Number = {2},
	Pages = {137--150},
	Pii = {0730-725X(95)02009-I},
	Pmid = {8847969},
	Timestamp = {2007.09.08},
	Title = {MRI of myocardial function: motion tracking techniques.},
	Volume = {14},
	Year = {1996}}

@article{Meegama2003,
	Author = {Ravinda G. N. Meegama and Jagath C. Rajapakse},
	Journal = {Image and Vision Computing},
	Number = {21},
	Owner = {tustison},
	Pages = {551-562},
	Title = {NURBS Snakes},
	Year = {2003}}

@inproceedings{Menet1990,
	Author = {Sylvie Menet and Philippe Saint-Marc and Gerard Medioni},
	Booktitle = {Image Understanding Workshop},
	Editor = {Darpa},
	Owner = {tustison},
	Pages = {720-726},
	Title = {B-snakes: implementation and application to stereo},
	Year = {1990}}

@article{Mentore2005,
	Abstract = {RATIONALE AND OBJECTIVES: The purpose of this study is to determine hyperpolarized helium 3 (HHe) magnetic resonance (MR) findings of the lung in patients with cystic fibrosis (CF) compared with healthy subjects and determine whether HHe MR can detect changes after bronchodilator therapy or mechanical airway mucus clearance treatment. MATERIALS AND METHODS: Thirty-one subjects, 16 healthy volunteers and 15 patients with CF, underwent HHe lung ventilation MR imaging and spirometry at baseline. Eight patients with CF then were treated with nebulized albuterol, after which a follow-up HHe MR scan was obtained. Subsequently, recombinant human deoxyribonuclease (DNase) treatment and chest physical therapy were performed in these eight subjects, followed by a third HHe MR scan. For each MR study, the number of ventilation defects was scored by a human reader. RESULTS: Patients with CF had significantly more HHe MR ventilation defects per image than healthy subjects (mean, 8.2 defects in patients with CF vs 1.6 defects in healthy subjects; P < .05). Even the four subjects with CF with a normal forced expiratory volume in 1 second had significantly more ventilation defects than healthy subjects (mean, 6.5 defects in these patients with CF; P = .0002). After treatment with albuterol, there was a small, but statistically significant, decrease in number of ventilation defects (mean, 9.6-8.0 defects; P = .025). After DNase and chest physical therapy, there was a trend toward increasing ventilation defects (mean, 8.3 defects; P = .096), but with a residual net improvement relative to baseline. CONCLUSION: In patients with CF, HHe MR ventilation defects correlate with spirometry, change with treatment, and are elevated in number in patients with CF with normal spirometry results. Thus, HHe MR appears to possess many of the characteristics required of a biomarker for pulmonary CF and may be useful in the evaluation of CF pulmonary disease severity or progression.},
	Author = {Kimiknu Mentore and Deborah K Froh and Eduard E de Lange and James R Brookeman and Alix O Paget-Brown and Talissa A Altes},
	Doi = {10.1016/j.acra.2005.07.008},
	Journal = {Acad Radiol},
	Keywords = {Administration, Inhalation; Adult; Albuterol; Bronchodilator Agents; Cystic Fibrosis; Deoxyribonuclease I; Female; Helium; Humans; Isotopes; Lung; Magnetic Resonance Imaging; Male; Pulmonary Ventilation; Recombinant Proteins; Respiratory Function Tests; Respiratory Therapy; Spirometry},
	Month = {Nov},
	Number = {11},
	Pages = {1423--1429},
	Pii = {S1076-6332(05)00647-1},
	Pmid = {16253854},
	Timestamp = {2007.06.06},
	Title = {Hyperpolarized HHe 3 MRI of the lung in cystic fibrosis: assessment at baseline and after bronchodilator and airway clearance treatment.},
	Url = {http://dx.doi.org/10.1016/j.acra.2005.07.008},
	Volume = {12},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.acra.2005.07.008}}

@article{Mergo1998,
	Author = {P. J. Mergo and W. F. Williams and R. Gonzalez-Rothi and R. Gibson and P. R. Ros and E. V. Staab and T. Helmberger},
	Journal = {AJR Am J Roentgenol},
	Month = {May},
	Number = {5},
	Pages = {1355--1360},
	Timestamp = {2009.05.18},
	Title = {Three-dimensional volumetric assessment of abnormally low attenuation of the lung from routine helical {CT}: inspiratory and expiratory quantification.},
	Volume = {170},
	Year = {1998}}

@article{Metaxas1993,
	Author = {Dimitri Metaxas and Demetri Terzopoulos},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {6},
	Owner = {tustison},
	Pages = {580-591},
	Title = {Shape and Nonrigid Motion Estimation through Physics-Based Synthesis},
	Volume = {15},
	Year = {1993}}

@article{Mezghani2008,
	Author = {Mezghani, N. and Mitiche, A. and Cheriet, M.},
	Doi = {10.1109/TPAMI.2007.70753},
	Journal = IEEE_J_PAMI,
	Month = {July},
	Number = {7},
	Pages = {1121--1131},
	Timestamp = {2008.11.26},
	Title = {Bayes Classification of Online Arabic Characters by Gibbs Modeling of Class Conditional Densities},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70753}}

@article{Miller1997,
	Author = {Michael Miller and Ayananshu Banerjee and Gary Christensen and Sarang Joshi and Navin Khaneja and Ulf Grenander and Larissa Matejic},
	Journal = {Statistical Methods in Medical Research},
	Owner = {tustison},
	Pages = {267-299},
	Title = {Statistical methods in computational anatomy},
	Volume = {6},
	Year = {1997}}

@article{Miller2005,
	Annote = {submitted},
	Author = {M. I. Miller and A. Trouv\`{e} and L. Younes},
	Journal = {J. Mathematical Imaging and Vision},
	Note = {submitted},
	Title = {Geodesic Shooting for Computational Anatomy},
	Year = {2005}}

@article{Miller2002,
	Abstract = {This paper reviews literature, current concepts and approaches in computational anatomy (CA). The model of CA is a Grenander deformable template, an orbit generated from a template under groups of diffeomorphisms. The metric space of all anatomical images is constructed from the geodesic connecting one anatomical structure to another in the orbit. The variational problems specifying these metrics are reviewed along with their associated Euler-Lagrange equations. The Euler equations of motion derived by Arnold for the geodesics in the group of divergence-free volume-preserving diffeomorphisms of incompressible fluids are generalized for the larger group of diffeomorphisms used in CA with nonconstant Jacobians. Metrics that accommodate photometric variation are described extending the anatomical model to incorporate the construction of neoplasm. Metrics on landmarked shapes are reviewed as well as Joshi's diffeomorphism metrics, Bookstein's thin-plate spline approximate-metrics, and Kendall's affine invariant metrics. We conclude by showing recent experimental results from the Toga & Thompson group in growth, the Van Essen group in macaque and human cortex mapping, and the Csernansky group in hippocampus mapping for neuropsychiatric studies in aging and schizophrenia.},
	Author = {Michael I Miller and Alain Trouve and Laurent Younes},
	Doi = {10.1146/annurev.bioeng.4.092101.125733},
	Journal = {Annu Rev Biomed Eng},
	Keywords = {Algorithms, Animals, Brain, Humans, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Macaca, Models, Neurological, Models, Statistical, Research Support, U.S. Gov't, Non-P.H.S., Research Support, U.S. Gov't, P.H.S., 12117763},
	Owner = {tustison},
	Pages = {375-405},
	Pii = {092101.125733},
	Title = {On the metrics and euler-lagrange equations of computational anatomy.},
	Url = {http://dx.doi.org/10.1146/annurev.bioeng.4.092101.125733},
	Volume = {4},
	Year = {2002},
	Bdsk-Url-1 = {http://dx.doi.org/10.1146/annurev.bioeng.4.092101.125733}}

@article{Miller2001,
	Author = {Michael I. Miller and Laurent Younes},
	Journal = {Internation Journal of Computer Vision},
	Number = {1/2},
	Owner = {tustison},
	Pages = {61-84},
	Title = {Group Actions, Homeomorphisms, and Matching: A General Framework},
	Volume = {41},
	Year = {2001}}

@article{Miller1989,
	Journal = {Am Rev Respir Dis},
	Month = {Apr},
	Number = {4},
	Pages = {980--983},
	Timestamp = {2009.05.18},
	Title = {Limitations of computed tomography in the assessment of emphysema.},
	Volume = {139},
	Year = {1989}}

@article{Mishima1999,
	Author = {M. Mishima and T. Hirai and H. Itoh and Y. Nakano and H. Sakai and S. Muro and K. Nishimura and Y. Oku and K. Chin and M. Ohi and T. Nakamura and J. H. Bates and A. M. Alencar and B. Suki},
	Journal = {Proc Natl Acad Sci U S A},
	Month = {Aug},
	Number = {16},
	Pages = {8829--8834},
	Timestamp = {2009.05.18},
	Title = {Complexity of terminal airspace geometry assessed by lung computed tomography in normal subjects and patients with chronic obstructive pulmonary disease.},
	Volume = {96},
	Year = {1999}}

@article{Mita2008,
	Author = {Mita, T. and Kaneko, T. and Stenger, B. and Hori, O.},
	Doi = {10.1109/TPAMI.2007.70767},
	Journal = IEEE_J_PAMI,
	Month = {July},
	Number = {7},
	Pages = {1257--1269},
	Timestamp = {2008.11.26},
	Title = {Discriminative Feature Co-Occurrence Selection for Object Detection},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70767}}

@article{Miyazawa2008,
	Author = {Miyazawa, K. and Ito, K. and Aoki, T. and Kobayashi, K. and Nakajima, H.},
	Doi = {10.1109/TPAMI.2007.70833},
	Journal = IEEE_J_PAMI,
	Month = {Oct.},
	Number = {10},
	Pages = {1741--1756},
	Timestamp = {2008.11.26},
	Title = {An Effective Approach for Iris Recognition Using Phase-Based Image Matching},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70833}}

@article{Miyazawa2006,
	Author = {Miyazawa, M. and Peifeng Zeng and Iso, N. and Hirata, T.},
	Doi = {10.1109/TPAMI.2006.133},
	Journal = IEEE_J_PAMI,
	Month = {July},
	Number = {7},
	Pages = {1127--1134},
	Timestamp = {2008.11.26},
	Title = {A systolic algorithm for Euclidean distance transform},
	Volume = {28},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2006.133}}

@article{Montaudon2007,
	Journal = {Radiology},
	Month = {Feb},
	Number = {2},
	Pages = {563--572},
	Timestamp = {2009.05.18},
	Title = {Assessment of airways with three-dimensional quantitative thin-section {CT}: in vitro and in vivo validation.},
	Volume = {242},
	Year = {2007}}

@inproceedings{Mortensen1995,
	Author = {E. N. Mortensen and W. A. Barrett},
	Booktitle = {PRoc. ACM SIGGRAPH 95: Computer Graphics and Interactive Techniques},
	Month = {August},
	Pages = {191-198},
	Timestamp = {2008.05.21},
	Title = {Intelligent Scissors for Image Composition},
	Year = {1995}}

@inproceedings{Mortensen1992,
	Author = {E. N. Mortensen and B. S. Morse and W. A. Barrett},
	Booktitle = {IEEE Proc. Computers in Cardiology},
	Pages = {635-638},
	Timestamp = {2008.05.21},
	Title = {Adaptive boundary detection using `live-wire' two-dimensional dynamic programming},
	Year = {1992}}

@article{Mosbah2006,
	Abstract = {PURPOSE: To demonstrate ventilation changes in an animal model of methacholine-induced bronchoconstriction using hyperpolarized (HP) helium-3 (He-3) MRI. MATERIALS AND METHODS: Bronchoconstriction was induced in 11 healthy rats using an intravenous injection of methacholine. The He-3 was laser-polarized using a custom-built system. MRI studies were performed on a 2-Tesla bore magnet. Coronal dynamic ventilation images were obtained using a single inhalation of the laser-polarized He-3 gas before and after methacholine injection. Ventilation image series were processed on a pixel-by-pixel basis to generate three regional ventilation parameters: gas flow rate, filling time, and maximum gas volume. Student's paired t-test was used for analysis. RESULTS: Ventilation image series with a temporal resolution of 5 msec were obtained before and after methacholine challenge. Quantitative regional gas dynamic information demonstrated statistically significant differences between the baseline and constricted states. Following methacholine injection, the mean flow values were significantly lower for the right lung (RL) (P = 0.006) and left lung (LL) (P = 0.024), while the mean filling time was found to be greater (RL: P = 0.08, LL: P = 0.021). Gas volume values at maximum inspiration were found to be significantly lower after methacholine (RL: P = 0.002; LL: P = 0.036). CONCLUSION: He-3 MRI demonstrated and quantified regional ventilation changes in bronchoconstriction conditions in rats.},
	Doi = {10.1002/jmri.20671},
	Journal = {J Magn Reson Imaging},
	Keywords = {Animals; Bronchoconstrictor Agents; Helium; Image Processing, Computer-Assisted; Lasers; Lung; Magnetic Resonance Imaging; Magnetics; Male; Methacholine Chloride; Models, Statistical; Rats; Rats, Sprague-Dawley; Time Factors},
	Month = {Sep},
	Number = {3},
	Pages = {611--616},
	Pmid = {16888775},
	Timestamp = {2007.06.06},
	Title = {Quantitative measurements of regional lung ventilation using helium-3 MRI in a methacholine-induced bronchoconstriction model.},
	Url = {http://dx.doi.org/10.1002/jmri.20671},
	Volume = {24},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/jmri.20671}}

@article{Mueller2002,
	Journal = {Thorax},
	Month = {Nov},
	Number = {11},
	Pages = {982--985},
	Timestamp = {2009.05.18},
	Title = {Chronic obstructive pulmonary disease. 4: imaging the lungs in patients with chronic obstructive pulmonary disease.},
	Volume = {57},
	Year = {2002}}

@article{Mueller1988,
	Journal = {Chest},
	Month = {Oct},
	Number = {4},
	Pages = {782--787},
	Timestamp = {2009.05.18},
	Title = {"Density mask". An objective method to quantitate emphysema using computed tomography.},
	Volume = {94},
	Year = {1988}}

@article{Mullikin1992,
	Author = {J. C. Mullikin},
	Journal = {CVGIP: Graphical Models and Image Processing},
	Owner = {tustison},
	Pages = {526-535},
	Title = {The Vector Distance Transform in Two and Three Dimensions},
	Volume = {54},
	Year = {1992}}

@article{Mumford1998,
	Author = {D. Mumford},
	Journal = {Questions Matheematiques En Traitement Du Signal et de L'Image, Institut Henri Poincare},
	Pages = {7-13},
	Title = {Pattern Theory and Vision},
	Volume = {3},
	Year = {1998}}

@inproceedings{Naher,
	Author = {Stefan Naher and Oliver Zlotowski},
	Owner = {tustison},
	Title = {Design and Implementation of Efficient Data Types for Static Graphs}}

@article{Najman2007,
	Author = {L. Najman and J. Cousty and M. Couprie and H. Talbot and S. Clement-Guinaudeau and T. Goissen and J. Garot},
	Journal = {Insight Journal},
	Month = {June},
	Timestamp = {2007.08.03},
	Title = {An open, clinically-validated database of 3D+t cine-{MR} images of the left ventricle with associated manual and automated segmentations},
	Url = {http://hdl.handle.net/1926/550},
	Year = {2007},
	Bdsk-Url-1 = {http://hdl.handle.net/1926/550}}

@article{Nakano2001,
	Journal = {Am J Respir Crit Care Med},
	Month = {Dec},
	Number = {12},
	Pages = {2195--2199},
	Timestamp = {2009.05.18},
	Title = {Core to rind distribution of severe emphysema predicts outcome of lung volume reduction surgery.},
	Volume = {164},
	Year = {2001}}

@article{Nakano2002,
	Journal = {Chest},
	Month = {Dec},
	Number = {6 Suppl},
	Pages = {271S--275S},
	Timestamp = {2009.05.18},
	Title = {Quantitative assessment of airway remodeling using high-resolution {CT}.},
	Volume = {122},
	Year = {2002}}

@article{Nakano2000,
	Journal = {Am J Respir Crit Care Med},
	Month = {Sep},
	Number = {3 Pt 1},
	Pages = {1102--1108},
	Timestamp = {2009.05.18},
	Title = {Computed tomographic measurements of airway dimensions and emphysema in smokers. Correlation with lung function.},
	Volume = {162},
	Year = {2000}}

@article{Nakano1999,
	Author = {Y. Nakano and H. Sakai and S. Muro and T. Hirai and Y. Oku and K. Nishimura and M. Mishima},
	Journal = {Thorax},
	Month = {May},
	Number = {5},
	Pages = {384--389},
	Timestamp = {2009.05.18},
	Title = {Comparison of low attenuation areas on computed tomographic scans between inner and outer segments of the lung in patients with chronic obstructive pulmonary disease: incidence and contribution to lung function.},
	Volume = {54},
	Year = {1999}}

@article{Nasiraei-Moghaddam2004,
	Abstract = {In this work the effects of noise, resolution, and velocity (flow) on the measurement of intravascular pressure from phase-contrast (PC) MRI are discussed. To elucidate these effects, we employed an axisymmetric geometry that enabled us to calculate pressures in <2 min on a Sun Ultra SPARC 10 workstation. To determine the effects of vascular stenoses, we fabricated several stenotic phantom geometries (with 50\%, 75\%, and 90\% area stenoses), and performed both MRI and computational fluid dynamics (CFD) simulations for various flow rates for these phantom geometries. Noise with Gaussian statistics was added to the velocity field obtained from the CFD simulations. The pressure maps obtained directly from CFD simulations for our phantom geometries were compared with pressure maps derived by our algorithm when 1) the input was noise-corrupted velocity data from CFD, and 2) the input was PC-MRI data collected from the phantoms. The quantitative effects of noise, resolution, and flow rate on the accuracy of pressure measurements were determined. We found that for flow rates below the Reynolds number for turbulent flow, resolution is a more significant determinant of accuracy than SNR. Furthermore, if other parameters remain constant, increased flow rates may result in decreased accuracy.},
	Author = {Abbas Nasiraei-Moghaddam and Geoffrey Behrens and Nasser Fatouraee and Ramesh Agarwal and Eric T Choi and Amir A Amini},
	Doi = {10.1002/mrm.20152},
	Journal = {Magn Reson Med},
	Keywords = {Algorithms, Blood Flow Velocity, Blood Pressure, Constriction, Pathologic, Hemorheology, Magnetic Resonance Imaging, Models, Cardiovascular, Phantoms, Imaging, Poisson Distribution, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S., Viscosity, 15282812},
	Month = {Aug},
	Number = {2},
	Owner = {tustison},
	Pages = {300-9},
	Title = {Factors affecting the accuracy of pressure measurements in vascular stenoses from phase-contrast {MRI}.},
	Url = {http://dx.doi.org/10.1002/mrm.20152},
	Volume = {52},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/mrm.20152}}

@article{Newell2002,
	Author = {John D Newell},
	Journal = {Radiol Clin North Am},
	Month = {Jan},
	Number = {1},
	Pages = {31--42, vii},
	Timestamp = {2009.05.18},
	Title = {{CT} of emphysema.},
	Volume = {40},
	Year = {2002}}

@article{Newell2004,
	Author = {J. D. Newell and J. C. Hogg and G. L. Snider},
	Journal = {Eur Respir J},
	Month = {May},
	Number = {5},
	Pages = {769--775},
	Timestamp = {2009.05.18},
	Title = {Report of a workshop: quantitative computed tomography scanning in longitudinal studies of emphysema.},
	Volume = {23},
	Year = {2004}}

@article{Newman1994,
	Abstract = {OBJECTIVE: The purpose of this study was to prospectively see if quantitative computed tomography (QCT) could separate asthmatic patients from normal control subjects. The QCT results were also correlated with the pulmonary function tests (PFT) that were done on both the asthmatic patients and control subjects. SUBJECTS AND METHODS: Eighteen adult nonsmoking asthmatics and 22 adult control subjects were entered into the study. Quantitative CT was performed at the level of the transverse aorta and just above the diaphragm at both end inspiration and end expiration in all patients and control subjects: 10-mm and 1.5-mm collimation using a high spatial frequency algorithm was used to obtain the QCT examinations. The percent of pixels below -900 Hounsfeld units, pixel index, in each of the QCT axial images of the lungs was calculated for each asthmatic and control subject in the study. Pulmonary function testing was performed on both the asthmatics and control subjects and included determination of FEV1, FVC, FRC, RV, and TLC. Unpaired Student's t test analysis of the QCT data was done to statistically compare the asthmatics with the control subjects. Linear regression analysis was done to compare the QCT results with PFT data on the asthmatics and control subjects. RESULTS: When scans were performed at end expiration, at a level immediately superior to the diaphragm, the mean pixel index was significantly higher in asthmatic subjects compared with normal individuals on both CT (mean for normal subjects 0.16 vs 4.45 for asthmatics, p < 0.004) and high-resolution CT (HRCT) images (mean for normal subjects 1.04 vs 10.03 in asthmatics, p < 0.0001) indicating more areas of low attenuation in asthmatics. The CT and HRCT images from the lower lung zones that were performed at end expiration provided the best separation between the groups. The pixel index on expiration correlated with the degree of air trapping and airflow limitation in the asthmatic group based on FEV1, FRC, RV, and to a lesser extent, FVC. CONCLUSION: Expiratory QCT is a useful method to assess air trapping in asthmatic patients. The percent of abnormal lung in asthmatics as determined by QCT has a significant correlation with the PFTs that reflect air trapping in asthmatic patients. Quantitative CT may be helpful in assessing degrees of air trapping present in other diseases affecting the airways.},
	Author = {K. B. Newman and D. A. Lynch and L. S. Newman and D. Ellegood and J. D. Newell},
	Journal = {Chest},
	Keywords = {Adult; Aged; Asthma; Female; Forced Expiratory Volume; Functional Residual Capacity; Humans; Lung; Male; Middle Aged; Prospective Studies; Residual Volume; Tomography, X-Ray Computed; Vital Capacity},
	Month = {Jul},
	Number = {1},
	Pages = {105--109},
	Pmid = {8020254},
	Timestamp = {2007.09.09},
	Title = {Quantitative computed tomography detects air trapping due to asthma.},
	Volume = {106},
	Year = {1994}}

@book{Ogden1997,
	Author = {R. W. Ogden},
	Publisher = {Dover Publications, Inc.},
	Timestamp = {2008.05.20},
	Title = {Non-Linear Elastic Deformation},
	Year = {1997}}

@article{Ooi2002,
	Author = {Gaik C Ooi and Pek L Khong and Moira Chan-Yeung and James C M Ho and Philip K S Chan and Jeriel C K Lee and Wah K Lam and Kenneth W T Tsang},
	Journal = {Radiology},
	Month = {Dec},
	Number = {3},
	Pages = {663--672},
	Timestamp = {2009.05.18},
	Title = {High-resolution {CT} quantification of bronchiectasis: clinical and functional correlation.},
	Volume = {225},
	Year = {2002}}

@article{Ooi2003,
	Author = {Gaik C Ooi and Kenneth W T Tsang and T. Fai Cheung and Pek L Khong and Iris W T Ho and Mary S M Ip and Chak M Tam and Henry Ngan and Wah K Lam and Fu L Chan and Moira Chan-Yeung},
	Journal = {Radiology},
	Month = {Sep},
	Number = {3},
	Pages = {816--825},
	Timestamp = {2009.05.18},
	Title = {Silicosis in 76 men: qualitative and quantitative {CT} evaluation--clinical-radiologic correlation study.},
	Volume = {228},
	Year = {2003}}

@article{Orlandi2004,
	Author = {Ilaria Orlandi and Chiara Moroni and Gianna Camiciottoli and Maurizio Bartolucci and Giacomo Belli and Natale Villari and Mario Mascalchi},
	Journal = {J Comput Assist Tomogr},
	Number = {4},
	Pages = {437--442},
	Timestamp = {2009.05.18},
	Title = {Spirometric-gated computed tomography quantitative evaluation of lung emphysema in chronic obstructive pulmonary disease: a comparison of 3 techniques.},
	Volume = {28},
	Year = {2004}}

@article{Orlandi2005,
	Author = {Ilaria Orlandi and Chiara Moroni and Gianna Camiciottoli and Maurizio Bartolucci and Massimo Pistolesi and Natale Villari and Mario Mascalchi},
	Journal = {Radiology},
	Month = {Feb},
	Number = {2},
	Pages = {604--610},
	Timestamp = {2009.05.18},
	Title = {Chronic obstructive pulmonary disease: thin-section {CT} measurement of airway wall thickness and lung attenuation.},
	Volume = {234},
	Year = {2005}}

@article{Osman2000,
	Abstract = {This paper describes a new image processing technique for rapid analysis and visualization of tagged cardiac magnetic resonance (MR) images. The method is based on the use of isolated spectral peaks in spatial modulation of magnetization (SPAMM)-tagged magnetic resonance images. We call the calculated angle of the complex image corresponding to one of these peaks a harmonic phase (HARP) image and show that HARP images can be used to synthesize conventional tag lines, reconstruct displacement fields for small motions, and calculate two-dimensional (2-D) strain. The performance of this new approach is demonstrated using both real and simulated tagged MR images. Potential for use of HARP images in fast imaging techniques and three-dimensional (3-D) analyses are discussed.},
	Author = {N. F. Osman and E. R. McVeigh and J. L. Prince},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Algorithms; Fourier Analysis; Heart; Humans; Image Processing, Computer-Assisted; Magnetic Resonance Imaging, Cine; Myocardial Contraction; Phantoms, Imaging; Reproducibility of Results},
	Month = {Mar},
	Number = {3},
	Pages = {186--202},
	Pmid = {10875703},
	Timestamp = {2007.12.20},
	Title = {Imaging heart motion using harmonic phase MRI.},
	Volume = {19},
	Year = {2000}}

@article{Ostrouchov2005,
	Author = {Ostrouchov, G. and Samatova, N.F.},
	Doi = {10.1109/TPAMI.2005.164},
	Journal = IEEE_J_PAMI,
	Month = {Aug.},
	Number = {8},
	Pages = {1340--1343},
	Timestamp = {2008.11.26},
	Title = {On FastMap and the convex hull of multivariate data: toward fast and robust dimension reduction},
	Volume = {27},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2005.164}}

@article{Othman2003,
	Author = {Othman, H. and Aboulnasr, T.},
	Doi = {10.1109/TPAMI.2003.1233897},
	Journal = IEEE_J_PAMI,
	Month = {Oct.},
	Number = {10},
	Pages = {1229--1238},
	Timestamp = {2008.11.26},
	Title = {A separable low complexity 2D HMM with application to face recognition},
	Volume = {25},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2003.1233897}}

@article{Otsu1979,
	Author = {N. Otsu},
	Journal = {IEEE Transactions on System, Man, and Cybernetics},
	Pages = {62-66},
	Timestamp = {2007.12.20},
	Title = {A thresholding selection method from gray-scale histogram},
	Volume = {9},
	Year = {1979}}

@inproceedings{Ozturk1999,
	Author = {C. Ozturk and E. R. McVeigh},
	Booktitle = {Proceedings SPIE Medical Imaging},
	Month = {February},
	Pages = {46-56},
	Publisher = {SPIE},
	Timestamp = {2007.09.09},
	Title = {Four dimensional B-spline based motion analysis of tagged cardiac MR images},
	Volume = {3660},
	Year = {1999}}

@article{Paganin1996,
	Abstract = {Airways remodelling is a feature of longstanding asthma, but may differ in persons with allergic and nonallergic asthma. To assess airways remodelling indirectly, we compared permanent CT-scan abnormalities in 70 subjects with allergic (median age: 30 yr) and 56 with nonallergic asthma (median age: 54.5 yr) who had had asthma of similar duration. None of the subjects were smokers. Asthma severity was assessed by Aas score and FEV1. Permanent high-resolution computed tomographic (HR-CT) scan abnormalities were characterized. In comparison with allergic asthmatic subjects, those with nonallergic asthma had a significantly greater frequency of cylindric (p < 0.0007, Mann-Whitney U test) and varicose (p < 0.004) bronchiectasis, emphysema (p < 0.0003), bronchial recruitment (p < 0.0001), and sequellar linear shadows (p < 0.0001). There was a significant correlation between Aas score and emphysema (p < 0.0001 for nonallergic and p < 0.0005 for allergic asthma; Kendall's test method) or Aas score and sequellar linear shadows (p < 0.007, nonallergic asthma). There was a significant increase in the extent of permanent abnormalities with increasing severity and duration of asthma in both groups. Patients with brittle asthma had few permanent abnormalities. This study confirms that after a similar course of the disease, patients with nonallergic asthma have a more extensive remodelling of the airways than those with allergic asthma.},
	Journal = {Am J Respir Crit Care Med},
	Keywords = {Adolescent; Adult; Aged; Analysis of Variance; Asthma; Bronchiectasis; Forced Expiratory Volume; Humans; Immunoglobulin E; Lung; Middle Aged; Pulmonary Emphysema; Radioallergosorbent Test; Tomography, X-Ray Computed},
	Month = {Jan},
	Number = {1},
	Pages = {110--114},
	Pmid = {8542102},
	Timestamp = {2007.09.09},
	Title = {Computed tomography of the lungs in asthma: influence of disease severity and etiology.},
	Volume = {153},
	Year = {1996}}

@article{Paige1982,
	Author = {Christopher C. Paige and Michael A. Saunders},
	Journal = {{ACM} Transactions on Mathematical Software},
	Month = {June},
	Number = {2},
	Pages = {195-209},
	Timestamp = {2007.06.18},
	Title = {{Algorithm 583}: {LSQR}: Sparse Linear Equations and Least Squares Problems},
	Url = {http://doi.acm.org/10.1145/355993.356000},
	Volume = {8},
	Year = {1982},
	Bdsk-Url-1 = {http://doi.acm.org/10.1145/355993.356000}}

@article{Palagyi2006,
	Journal = {Comput Biol Med},
	Month = {Sep},
	Number = {9},
	Pages = {974--996},
	Timestamp = {2009.05.18},
	Title = {Quantitative analysis of pulmonary airway tree structures.},
	Volume = {36},
	Year = {2006}}

@article{Pan2003,
	Author = {Zhihong Pan and Healey, G. and Prasad, M. and Tromberg, B.},
	Doi = {10.1109/TPAMI.2003.1251148},
	Journal = IEEE_J_PAMI,
	Month = {Dec.},
	Number = {12},
	Pages = {1552--1560},
	Timestamp = {2008.11.26},
	Title = {Face recognition in hyperspectral images},
	Volume = {25},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2003.1251148}}

@book{Papoulis2001,
	Author = {P. Papoulis and S. U. Pillai},
	Publisher = {McGraw-Hill},
	Timestamp = {2008.08.14},
	Title = {Probabilty, Random Variables, and Stochastic Processes},
	Year = {2001}}

@article{Park1999,
	Author = {K. J. Park and C. J. Bergin and J. L. Clausen},
	Journal = {Radiology},
	Month = {May},
	Number = {2},
	Pages = {541--547},
	Timestamp = {2009.05.18},
	Title = {Quantitation of emphysema with three-dimensional {CT} densitometry: comparison with two-dimensional analysis, visual emphysema scores, and pulmonary function test results.},
	Volume = {211},
	Year = {1999}}

@article{Park1998,
	Author = {W. Park and E. A. Hoffman and M. Sonka},
	Journal = {IEEE Trans Med Imaging},
	Month = {Aug},
	Number = {4},
	Pages = {489--497},
	Timestamp = {2009.05.18},
	Title = {Segmentation of intrathoracic airway trees: a fuzzy logic approach.},
	Volume = {17},
	Year = {1998}}

@article{Parr2004,
	Author = {David G Parr and Berend C Stoel and Jan Stolk and Peter G Nightingale and Robert A Stockley},
	Journal = {Am J Respir Crit Care Med},
	Month = {Oct},
	Number = {8},
	Pages = {883--890},
	Timestamp = {2009.05.18},
	Title = {Influence of calibration on densitometric studies of emphysema progression using computed tomography.},
	Volume = {170},
	Year = {2004}}

@article{Parraga2007,
	Abstract = {OBJECTIVE:: Hyperpolarized He magnetic resonance imaging (He MRI) at 3.0 Tesla of healthy volunteers and chronic obstructive pulmonary disease (COPD) patients was performed for quantitative evaluation of ventilation defects and apparent diffusion coefficients (ADC) and for comparison to published results acquired at 1.5 Tesla. The reproducibility of He ADC and ventilation defects was also assessed in subjects scanned 3 times, twice within 10 minutes, and again within 7 +/- 2 days of the first MRI visit. MATERIALS AND METHODS:: Hyperpolarized He MRI was performed in 6 subjects. Two interleaved images with and without additional diffusion sensitization were acquired with the first image serving as a ventilation image from which defect score and volume were measured and the combination of the 2 images used to compute ADC maps and ADC histograms. RESULTS:: He MRI at 3.0 Tesla showed increased mean ADC and ADC standard deviation for subjects with COPD compared with healthy volunteers (ADC healthy volunteer (0.24 +/- 0.12 cm/s), mild-moderate COPD (0.34 +/- 0.14 cm/s), and severe COPD (0.47 +/- 0.21 cm/s), and these values were similar to previously reported results acquired at 1.5 Tesla. Reproducibility of mean ADC was high (coefficient of variation 2\% in severe COPD, 3\% in mild-moderate COPD, 4\% in healthy volunteers) across all 3 scans. Higher same-day scan reproducibility was observed for ventilation defect volume compared with 1-week scan reproducibility in this small group of subjects. CONCLUSIONS:: ADC values for emphysematous lungs were significantly increased compared with healthy lungs in age-matched subjects, and all values were comparable to those reported previously at 1.5 Tesla. Ventilation defect score and ventilation defect volume results were also comparable to results previously reported in COPD subjects Reproducibility of ADC for same-day scan-rescan and 7-day rescan was high and similar to previously reported results.},
	Author = {Grace Parraga and Alexei Ouriadov and Andrea Evans and Shayna McKay and Wilfred Lam and Aaron Fenster and Roya Etemad-Rezai and David McCormack and Giles Santyr},
	Doi = {10.1097/01.rli.0000262571.81771.66},
	Journal = {Invest Radiol},
	Month = {Jun},
	Number = {6},
	Pages = {384--391},
	Pii = {00004424-200706000-00008},
	Pmid = {17507809},
	Timestamp = {2007.06.06},
	Title = {Hyperpolarized 3He Ventilation Defects and Apparent Diffusion Coefficients in Chronic Obstructive Pulmonary Disease: Preliminary Results at 3.0 Tesla.},
	Url = {http://dx.doi.org/10.1097/01.rli.0000262571.81771.66},
	Volume = {42},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1097/01.rli.0000262571.81771.66}}

@article{Passalis2007,
	Author = {Passalis, G. and Kakadiaris, I.A. and Theoharis, T.},
	Doi = {10.1109/TPAMI.2007.37},
	Journal = IEEE_J_PAMI,
	Month = {Feb.},
	Number = {2},
	Pages = {218--229},
	Timestamp = {2008.11.26},
	Title = {Intraclass Retrieval of Nonrigid 3D Objects: Application to Face Recognition},
	Volume = {29},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.37}}

@article{Patel2006,
	Author = {Bip Patel and Barry Make and Harvey O Coxson and Nestor L Muller and Sreekumar Pillai and Wayne Anderson and Edwin Silverman and David Lomas},
	Journal = {Proc Am Thorac Soc},
	Month = {Aug},
	Number = {6},
	Pages = {533},
	Timestamp = {2009.05.18},
	Title = {Airway and parenchymal disease in chronic obstructive pulmonary disease are distinct phenotypes.},
	Volume = {3},
	Year = {2006}}

@article{Pattichis2007,
	Author = {Pattichis, M.S. and Bovik, A.C.},
	Doi = {10.1109/TPAMI.2007.1051},
	Journal = IEEE_J_PAMI,
	Month = {May},
	Number = {5},
	Pages = {753--766},
	Timestamp = {2008.11.26},
	Title = {Analyzing Image Structure by Multidimensional Frequency Modulation},
	Volume = {29},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.1051}}

@techreport{Pennec1998,
	Author = {Xavier Pennec},
	Institution = {INRIA},
	Month = {March},
	Owner = {tustison},
	Title = {Computing the mean of geometric features: Application to the mean rotation},
	Year = {1998}}

@article{Pennec1998a,
	Author = {Xavier Pennec and Nicholas Ayache},
	Journal = {Journal of Mathematical Imaging and Vision},
	Number = {9},
	Owner = {tustison},
	Title = {Uniform Distribution, Distance and Expectation Problems for Geometric Features Processing},
	Volume = {9},
	Year = {1998}}

@article{Pennec2006,
	Author = {Xavier Pennec and Pierre Fillard and Nicholas Ayache},
	Journal = {International Journal of Computer Vision},
	Number = {1},
	Owner = {tustison},
	Pages = {41-66},
	Title = {A Riemannian Framework for Tensor Computing},
	Volume = {66},
	Year = {2006}}

@article{Penney1998,
	Abstract = {A comparison of six similarity measures for use in intensity-based two-dimensional-three-dimensional (2-D-3-D) image registration is presented. The accuracy of the similarity measures are compared to a "gold-standard" registration which has been accurately calculated using fiducial markers. The similarity measures are used to register a computed tomography (CT) scan of a spine phantom to a fluoroscopy image of the phantom. The registration is carried out within a region-of-interest in the fluoroscopy image which is user defined to contain a single vertebra. Many of the problems involved in this type of registration are caused by features which were not modeled by a phantom image alone. More realistic "gold-standard" data sets were simulated using the phantom image with clinical image features overlaid. Results show that the introduction of soft-tissue structures and interventional instruments into the phantom image can have a large effect on the performance of some similarity measures previously applied to 2-D-3-D image registration. Two measures were able to register accurately and robustly even when soft-tissue structures and interventional instruments were present as differences between the images. These measures were pattern intensity and gradient difference. Their registration accuracy, for all the rigid-body parameters except for the source to film translation, was within a root-mean-square (rms) error of 0.54 mm or degrees to the "gold-standard" values. No failures occurred while registering using these measures.},
	Author = {GP Penney and J Weese and JA Little and P Desmedt and DL Hill and DJ Hawkes},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Algorithms, Comparative Study, Fluoroscopy, Humans, Phantoms, Imaging, Research Support, Non-U.S. Gov't, Spine, Tomography, X-Ray Computed, 9845314},
	Month = {Aug},
	Number = {4},
	Owner = {tustison},
	Pages = {586-95},
	Title = {A comparison of similarity measures for use in 2-{D}-3-{D} medical image registration.},
	Volume = {17},
	Year = {1998}}

@article{Pereya2003,
	Author = {V. Pereya and G. Scherer},
	Journal = {Applied Numerical Mathematics},
	Number = {44},
	Owner = {tustison},
	Pages = {225-239},
	Title = {Large scale least squares scattered data fitting},
	Year = {2003}}

@article{Perez2005,
	Author = {Andrew Perez and Harvey O Coxson and James C Hogg and Kevin Gibson and Paul F Thompson and Robert M Rogers},
	Journal = {Chest},
	Month = {Oct},
	Number = {4},
	Pages = {2471--2477},
	Timestamp = {2009.05.18},
	Title = {Use of {CT} morphometry to detect changes in lung weight and gas volume.},
	Volume = {128},
	Year = {2005}}

@article{Perona1990,
	Author = {P. Perona and J. Malik},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {7},
	Pages = {629--639},
	Timestamp = {2009.03.11},
	Title = {Scale-Space and Edge Detection Using Anisotropic Diffusion},
	Volume = {12},
	Year = {1990}}

@article{Perronnin2008,
	Author = {Perronnin, F.},
	Doi = {10.1109/TPAMI.2007.70755},
	Journal = IEEE_J_PAMI,
	Month = {July},
	Number = {7},
	Pages = {1243--1256},
	Timestamp = {2008.11.26},
	Title = {Universal and Adapted Vocabularies for Generic Visual Categorization},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70755}}

@article{Pham1999,
	Author = {Dzung L. Pham and Jerry L. Prince},
	Journal = {IEEE Transactions on Medical Imaging},
	Number = {9},
	Owner = {tustison},
	Pages = {737-751},
	Title = {Adaptive Fuzzy Segmentation of Magnetic Resonance Images},
	Volume = {18},
	Year = {1999}}

@book{Piegl1997a,
	Author = {Les Piegl and Wayne Tiller},
	Owner = {tustison},
	Publisher = {Springer},
	Title = {The NURBS Book},
	Year = {1997}}

@article{Pizer2003,
	Author = {SM Pizer and PT Fletcher and S Joshi and A Thall and JZ Chen and Y Fridman and DS Fritsch and AG Gash and JM Glotzer and MR Jiroutek and C Lu and KE Muller and G Tracton and P Yushkevic and EL Cheney},
	Journal = {International Journal of Computer Vision},
	Number = {2/3},
	Owner = {tustison},
	Pages = {85-106},
	Title = {Deformable M-Reps for 3D Medical Image Segmentation},
	Volume = {55},
	Year = {2003}}

@article{Plass1983,
	Author = {Michael Plass and Maureen Stone},
	Journal = {Computer Graphics},
	Number = {3},
	Owner = {tustison},
	Pages = {229-239},
	Title = {Computer Graphics},
	Volume = {17},
	Year = {1983}}

@article{Pluim2004,
	Abstract = {A measure for registration of medical images that currently draws much attention is mutual information. The measure originates from information theory, but has been shown to be successful for image registration as well. Information theory, however, offers many more measures that may be suitable for image registration. These all measure the divergence of the joint distribution of the images' grey values from the joint distribution that would have been found had the images been completely independent. This paper compares the performance of mutual information as a registration measure with that of other F-information measures. The measures are applied to rigid registration of positron emission tomography (PET)/magnetic resonance (MR) and MR/computed tomography (CT) images, for 35 and 41 image pairs, respectively. An accurate gold standard transformation is available for the images, based on implanted markers. The registration performance, robustness and accuracy of the measures are studied. Some of the measures are shown to perform poorly on all aspects. The majority of measures produces results similar to those of mutual information. An important finding, however, is that several measures, although slightly more difficult to optimize, can potentially yield significantly more accurate results than mutual information.},
	Author = {Josien P W Pluim and J B Antoine Maintz and Max A Viergever},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Algorithms, Artificial Intelligence, Brain, Comparative Study, Computer Simulation, Diagnostic Imaging, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Information Storage and Retrieval, Magnetic Resonance Imaging, Models, Biological, Models, Statistical, Numerical Analysis, Computer-Assisted, Pattern Recognition, Automated, Positron-Emission Tomography, Reproducibility of Results, Research Support, Non-U.S. Gov't, Sensitivity and Specificity, Signal Processing, Computer-Assisted, Subtraction Technique, Tomography, X-Ray Computed, 15575408},
	Month = {Dec},
	Number = {12},
	Owner = {tustison},
	Pages = {1508-16},
	Title = {F-information measures in medical image registration.},
	Volume = {23},
	Year = {2004}}

@article{Pluim2003,
	Abstract = {An overview is presented of the medical image processing literature on mutual-information-based registration. The aim of the survey is threefold: an introduction for those new to the field, an overview for those working in the field, and a reference for those searching for literature on a specific application. Methods are classified according to the different aspects of mutual-information-based registration. The main division is in aspects of the methodology and of the application. The part on methodology describes choices made on facets such as preprocessing of images, gray value interpolation, optimization, adaptations to the mutual information measure, and different types of geometrical transformations. The part on applications is a reference of the literature available on different modalities, on interpatient registration and on different anatomical objects. Comparison studies including mutual information are also considered. The paper starts with a description of entropy and mutual information and it closes with a discussion on past achievements and some future challenges.},
	Author = {Josien P W Pluim and J B Antoine Maintz and Max A Viergever},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Algorithms, Anatomy, Cross-Sectional, Comparative Study, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Pattern Recognition, Automated, Research Support, Non-U.S. Gov't, Subtraction Technique, 12906253},
	Month = {Aug},
	Number = {8},
	Owner = {tustison},
	Pages = {986-1004},
	Title = {Mutual-information-based registration of medical images: a survey.},
	Volume = {22},
	Year = {2003}}

@conference{Pluta2008,
	Author = {John Pluta and Brian B. Avants and Simon Glynn and Suyash Awate and James C. Gee and John A. Detre},
	Booktitle = {MICCAI 2008 Workshop on Computational Anatomy and Physiology of the Hippocampus (CAPH'08)},
	Pages = {105--116},
	Title = {Appearance and Incomplete Label Matching for Diffeomorphic Template Based Hippocampus Segmentation},
	Url = {http://picsl.upenn.edu/caph08/papers/paper14.pdf},
	Year = {2008},
	Bdsk-Url-1 = {http://picsl.upenn.edu/caph08/papers/paper14.pdf}}

@article{Poggio1985,
	Author = {Tomaso Poggio and Vincent Torre and Christof Koch},
	Journal = {Nature},
	Owner = {tustison},
	Pages = {314-319},
	Title = {Computational vision and regularization theory},
	Volume = {317},
	Year = {1985}}

@book{Press1992,
	Author = {William H. Press and Brian P. Flannery and Saul A. Teukolsky and William T. Vetterling},
	Edition = {2},
	Publisher = {Cambridge University Press},
	Timestamp = {2007.06.18},
	Title = {Numerical Recipes: The Art of Scientific Computing},
	Year = {1992}}

@article{Provenzi2008,
	Author = {Provenzi, E. and Gatta, C. and Fierro, M. and Rizzi, A.},
	Doi = {10.1109/TPAMI.2007.70827},
	Journal = IEEE_J_PAMI,
	Month = {Oct.},
	Number = {10},
	Pages = {1757--1770},
	Timestamp = {2008.11.26},
	Title = {A Spatially Variant White-Patch and Gray-World Method for Color Image Enhancement Driven by Local Contrast},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70827}}

@article{Pun2003,
	Author = {Chi-Man Pun and Moon-Chuen Lee},
	Doi = {10.1109/TPAMI.2003.1195993},
	Journal = IEEE_J_PAMI,
	Month = {May},
	Number = {5},
	Pages = {590--603},
	Timestamp = {2008.11.26},
	Title = {Log-polar wavelet energy signatures for rotation and scale invariant texture classification},
	Volume = {25},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2003.1195993}}

@inproceedings{Qian2006,
	Author = {Zhen Qian and Dimitris N. Metaxas and Leon Axel},
	Booktitle = {Proceedings of the 28th IEEE-EMBS Annual International Conference},
	Timestamp = {2007.12.11},
	Title = {Extraction and Tracking of {MRI} Tagging Sheets Using a {3D} {G}abor Filter Bank},
	Year = {2006}}

@inproceedings{Qian2003,
	Author = {Zhen Qian and Albert Montillo and Dimitris N. Metaxas and Leon Axel},
	Booktitle = {Proceeedings of the 25ht Annual International Conference of the IEEE-EMBS},
	Timestamp = {2007.12.11},
	Title = {Segmenting Cardiac {MRI} Tagging Lines Using {G}abor Filter Banks},
	Year = {2003}}

@article{Qin1997,
	Author = {Hong Qin and Demetri Terzopoulos},
	Journal = {Computer Aided Geometric Design},
	Number = {14},
	Owner = {tustison},
	Pages = {325-347},
	Title = {Triangular NURBS and their dynamic generalizations},
	Year = {1997}}

@article{Qin1996,
	Author = {Hong Qin and Demetri Terzopoulos},
	Journal = {IEEE Transactions on Visualization and Computer Graphics},
	Number = {1},
	Owner = {tustison},
	Pages = {85-96},
	Title = {D-NURBS: A Physics-Based Framework for Geometric Design},
	Volume = {2},
	Year = {1996}}

@article{Quo2007,
	Author = {Yanlin Quo and Hsu, S. and Sawhney, H.S. and Kumar, R. and Ying Shan},
	Doi = {10.1109/TPAMI.2007.1052},
	Journal = IEEE_J_PAMI,
	Month = {May},
	Number = {5},
	Pages = {824--839},
	Timestamp = {2008.11.26},
	Title = {Robust Object Matching for Persistent Tracking with Heterogeneous Features},
	Volume = {29},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.1052}}

@article{Ragnemalm1993,
	Author = {I. Ragnemalm},
	Journal = {Pattern Recognition Letters},
	Owner = {tustison},
	Pages = {883-888},
	Title = {The Euclidean Distance Transform in Arbitrary Dimensions},
	Volume = {14},
	Year = {1993}}

@inproceedings{Ramaswami2003,
	Author = {S. Ramaswami and M. Siqueira and T.A.Sundaram and J. Gallier and J.C. Gee},
	Booktitle = {Proc. of the 12th International Meshing Roundtable},
	Timestamp = {2009.05.18},
	Title = {A New Algorithm for Generating Quadrilateral Meshes and its Application to {FE}-Based Image Registration},
	Year = {2003}}

@techreport{Ramshaw1989,
	Author = {Lyle Ramshaw},
	Institution = {Digital Systems Research Center},
	Owner = {tustison},
	Title = {Blossoms are Polar Forms},
	Year = {1989}}

@inproceedings{Randrianarivony2002,
	Author = {M. Randrianarivony and G. Brunnett},
	Booktitle = {VMV},
	Owner = {tustison},
	Title = {Approximation by NURBS curves with free knots},
	Year = {2002}}

@inproceedings{Rangarajan1997,
	Author = {Anand Rangarajan and Haili Chui and Fred L. Bookstein},
	Booktitle = {Proceedings of Information Processing in Medical Imaging},
	Pages = {29--42},
	Publisher = {Springer},
	Timestamp = {2008.09.03},
	Title = {The {S}oftassign {P}rocrustes matching algorithms},
	Year = {1997}}

@article{Rao2007,
	Author = {Hengyi Rao and Jiongjiong Wang and Joan Giannetta and Marc Korczykowski and David Shera and Brian B Avants and James Gee and John A Detre and Hallam Hurt},
	Journal = {Pediatrics},
	Month = {Nov},
	Number = {5},
	Pages = {e1245--e1254},
	Timestamp = {2009.05.18},
	Title = {Altered resting cerebral blood flow in adolescents with in utero cocaine exposure revealed by perfusion functional {MRI}.},
	Volume = {120},
	Year = {2007}}

@article{Rappoport1996,
	Author = {Ari Rappoport and Alla Sheffer and Michel Bercovier},
	Journal = {IEEE Transactions on Visualization and Computer Graphics},
	Number = {1},
	Owner = {tustison},
	Pages = {19-27},
	Title = {Volume-Preserving Free-Form Solids},
	Volume = {2},
	Year = {1996}}

@article{Ray2004,
	Author = {Nilanjan Ray and Scott T. Acton},
	Journal = {IEEE Transactions on Medical Imaging},
	Number = {12},
	Owner = {tustison},
	Pages = {1466-1478},
	Title = {Motion Gradient Vector Flow: An External Force for Tracking Rolling Leukocytes With Shape and Size Constrained Active Contours},
	Volume = {23},
	Year = {2004}}

@article{Raykar2008,
	Author = {Raykar, V.C. and Duraiswami, R. and Krishnapuram, B.},
	Doi = {10.1109/TPAMI.2007.70776},
	Journal = IEEE_J_PAMI,
	Month = {July},
	Number = {7},
	Pages = {1158--1170},
	Timestamp = {2008.11.26},
	Title = {A Fast Algorithm for Learning a Ranking Function from Large-Scale Data Sets},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70776}}

@article{Reddy2008,
	Author = {Reddy, C.K. and Hsiao-Dong Chiang and Rajaratnam, B.},
	Doi = {10.1109/TPAMI.2007.70775},
	Journal = IEEE_J_PAMI,
	Month = {July},
	Number = {7},
	Pages = {1146--1157},
	Timestamp = {2008.11.26},
	Title = {TRUST-TECH-Based Expectation Maximization for Learning Finite Mixture Models},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70775}}

@article{Reinhardt2007,
	Author = {Joseph M Reinhardt and Gary E Christensen and Eric A Hoffman and Kai Ding and Kunlin Cao},
	Journal = {Inf Process Med Imaging},
	Pages = {763--774},
	Timestamp = {2009.05.18},
	Title = {Registration-derived estimates of local lung expansion as surrogates for regional ventilation.},
	Volume = {20},
	Year = {2007}}

@article{Reinhardt1997,
	Author = {J. M. Reinhardt and N. D. D'Souza and E. A. Hoffman},
	Journal = {IEEE Trans Med Imaging},
	Month = {Dec},
	Number = {6},
	Pages = {820--827},
	Timestamp = {2009.05.18},
	Title = {Accurate measurement of intrathoracic airways.},
	Volume = {16},
	Year = {1997}}

@article{Reinhardt1998,
	Author = {J. M. Reinhardt and E. A. Hoffman},
	Journal = {Acad Radiol},
	Month = {Aug},
	Number = {8},
	Pages = {539--546},
	Timestamp = {2009.05.18},
	Title = {Quantitative pulmonary imaging: spatial and temporal considerations in high-resolution {CT}.},
	Volume = {5},
	Year = {1998}}

@article{Remme2005,
	Abstract = {We present a method to estimate left ventricular (LV) motion based on three-dimensional (3-D) images that can be derived from any anatomical tomographic or 3-D modality, such as echocardiography, computed tomography, or magnetic resonance imaging. A finite element mesh of the LV was constructed to fit the geometry of the wall. The mesh was deformed by optimizing the nodal parameters to the motion of a sparse number of fiducial markers that were manually tracked in the images through the cardiac cycle. A parameter distribution model (PDM) of LV deformations was obtained from a database of MR tagging studies. This was used to filter the calculated deformation and incorporate a priori information on likely motions. The estimated deformation obtained from 13 normal untagged studies was compared with the deformation obtained from MR tagging. The end systolic (ES) circumferential and longitudinal strain values matched well with a mean difference of 0.1 +/- 3.2\% and 0.3 +/- 3.0\%, respectively. The calculated apex-base twist angle at ES had a mean difference of 1.0 +/- 2.3 degrees. We conclude that fiducial marker fitting in conjunction with a PDM provides accurate reconstruction of LV deformation in normal subjects.},
	Author = {Espen W Remme and Kevin F Augenstein and Alistair A Young and Peter J Hunter},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Adult, Algorithms, Artificial Intelligence, Computer Simulation, Elasticity, Feasibility Studies, Female, Heart Ventricles, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Magnetic Resonance Imaging, Cine, Male, Models, Cardiovascular, Models, Statistical, Pattern Recognition, Automated, Reproducibility of Results, Research Support, Non-U.S. Gov't, Sensitivity and Specificity, Signal Processing, Computer-Assisted, Statistical Distributions, Stroke Volume, Subtraction Technique, Ventricular Function, Left, 15754988},
	Month = {Mar},
	Number = {3},
	Owner = {tustison},
	Pages = {381-8},
	Title = {Parameter distribution models for estimation of population based left ventricular deformation using sparse fiducial markers.},
	Volume = {24},
	Year = {2005}}

@article{Rieger2004,
	Author = {Rieger, B. and Timmermans, F.J. and van Vliet, L.J. and Verbeek, P.W.},
	Doi = {10.1109/TPAMI.2004.50},
	Journal = IEEE_J_PAMI,
	Month = {Aug.},
	Number = {8},
	Pages = {1088--1094},
	Timestamp = {2008.11.26},
	Title = {On curvature estimation of ISO surfaces in 3D gray-value images and the computation of shape descriptors},
	Volume = {26},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2004.50}}

@phdthesis{Riesenfeld1975,
	Author = {R. F. Riesenfeld},
	Owner = {tustison},
	School = {Syracuse University},
	Timestamp = {2006.12.20},
	Title = {Applications of B-Spline Approximation to Geometric Problems of Computer-Aided Design},
	Year = {1975}}

@article{Rodarte1985,
	Author = {Joseph R. Rodarte and Rolf D. Hubmayr and Dimitrije Stamenovic and Bruce J. Walters},
	Journal = {Journal of Applied Physiology},
	Number = {1},
	Owner = {tustison},
	Pages = {164-172},
	Title = {Regional lung strain in dogs during deflation from total lung capacity},
	Volume = {58},
	Year = {1985}}

@article{Rogers2000,
	Author = {R. M. Rogers and H. O. Coxson and F. C. Sciurba and R. J. Keenan and K. P. Whittall and J. C. Hogg},
	Journal = {Chest},
	Month = {Nov},
	Number = {5},
	Pages = {1240--1247},
	Timestamp = {2009.05.18},
	Title = {Preoperative severity of emphysema predictive of improvement after lung volume reduction surgery: use of {CT} morphometry.},
	Volume = {118},
	Year = {2000}}

@article{Rohlfing2003,
	Abstract = {In this paper, we extend a previously reported intensity-based nonrigid registration algorithm by using a novel regularization term to constrain the deformation. Global motion is modeled by a rigid transformation while local motion is described by a free-form deformation based on B-splines. An information theoretic measure, normalized mutual information, is used as an intensity-based image similarity measure. Registration is performed by searching for the deformation that minimizes a cost function consisting of a weighted combination of the image similarity measure and a regularization term. The novel regularization term is a local volume-preservation (incompressibility) constraint, which is motivated by the assumption that soft tissue is incompressible for small deformations and short time periods. The incompressibility constraint is implemented by penalizing deviations of the Jacobian determinant of the deformation from unity. We apply the nonrigid registration algorithm with and without the incompressibility constraint to precontrast and post-contrast magnetic resonance (MR) breast images from 17 patients. Without using a constraint, the volume of contrast-enhancing lesions decreases by 1\%-78\% (mean 26\%). Image improvement (motion artifact reduction) obtained using the new constraint is compared with that obtained using a smoothness constraint based on the bending energy of the coordinate grid by blinded visual assessment of maximum intensity projections of subtraction images. For both constraints, volume preservation improves, and motion artifact correction worsens, as the weight of the constraint penalty term increases. For a given volume change of the contrast-enhancing lesions (2\% of the original volume), the incompressibility constraint reduces motion artifacts better than or equal to the smoothness constraint in 13 out of 17 cases (better in 9, equal in 4, worse in 4). The preliminary results suggest that incorporation of the incompressibility regularization term improves intensity-based free-form nonrigid registration of contrast-enhanced MR breast images by greatly reducing the problem of shrinkage of contrast-enhancing structures while simultaneously allowing motion artifacts to be substantially reduced.},
	Author = {Torsten Rohlfing and Calvin R Maurer and David A Bluemke and Michael A Jacobs},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Adolescent, Aged, Aged, 80 and over, Algorithms, Artifacts, Breast Neoplasms, Comparative Study, Female, Humans, Image Enhancement, Imaging, Three-Dimensional, Magnetic Resonance Imaging, Middle Aged, Motion, Quality Control, Reproducibility of Results, Research Support, U.S. Gov't, Non-P.H.S., Sensitivity and Specificity, Single-Blind Method, Subtraction Technique, 12872948},
	Month = {Jun},
	Number = {6},
	Owner = {tustison},
	Pages = {730-41},
	Title = {Volume-preserving nonrigid registration of {MR} breast images using free-form deformation with an incompressibility constraint.},
	Volume = {22},
	Year = {2003}}

@article{Rohr2001,
	Abstract = {We consider elastic image registration based on a set of corresponding anatomical point landmarks and approximating thin-plate splines. This approach is an extension of the original interpolating thin-plate spline approach and allows to take into account landmark localization errors. The extension is important for clinical applications since landmark extraction is always prone to error. Our approach is based on a minimizing functional and can cope with isotropic as well as anisotropic landmark errors. In particular, in the latter case it is possible to include different types of landmarks, e.g., unique point landmarks as well as arbitrary edge points. Also, the scheme is general with respect to the image dimension and the order of smoothness of the underlying functional. Optimal affine transformations as well as interpolating thin-plate splines are special cases of this scheme. To localize landmarks we use a semi-automatic approach which is based on three-dimensional (3-D) differential operators. Experimental results are presented for two-dimensional as well as 3-D tomographic images of the human brain.},
	Author = {K. Rohr and H. S. Stiehl and R. Sprengel and T. M. Buzug and J. Weese and M. H. Kuhn},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Algorithms; Anatomy, Cross-Sectional; Brain; Humans; Image Processing, Computer-Assisted; Imaging, Three-Dimensional; Magnetic Resonance Imaging; Signal Processing, Computer-Assisted; Tomography, X-Ray Computed},
	Month = {Jun},
	Number = {6},
	Pages = {526--534},
	Pmid = {11437112},
	Timestamp = {2007.10.22},
	Title = {Landmark-based elastic registration using approximating thin-plate splines.},
	Volume = {20},
	Year = {2001}}

@article{Rose2000,
	Author = {Kenneth Rose},
	Citeseercitationcount = {0},
	Citeseerurl = {http://citeseer.ist.psu.edu/390030.html},
	Journal = {Proceedings of the IEEE},
	Number = {11},
	Pages = {2210-2239},
	Timestamp = {2007.12.12},
	Title = {Deterministic Annealing for Clustering, Compression, Classification, Regression, and Related Optimization Problems},
	Volume = {86},
	Year = {2000},
	Bdsk-Url-1 = {http://citeseer.ist.psu.edu/390030.html}}

@book{rosen2004open,
	Author = {Rosen, Lawrence},
	Owner = {stnava},
	Publisher = {Prentice Hall PTR},
	Timestamp = {2014.04.29},
	Title = {Open source licensing},
	Year = {2004}}

@article{Rueckert1999,
	Abstract = {In this paper we present a new approach for the nonrigid registration of contrast-enhanced breast MRI. A hierarchical transformation model of the motion of the breast has been developed. The global motion of the breast is modeled by an affine transformation while the local breast motion is described by a free-form deformation (FFD) based on B-splines. Normalized mutual information is used as a voxel-based similarity measure which is insensitive to intensity changes as a result of the contrast enhancement. Registration is achieved by minimizing a cost function, which represents a combination of the cost associated with the smoothness of the transformation and the cost associated with the image similarity. The algorithm has been applied to the fully automated registration of three-dimensional (3-D) breast MRI in volunteers and patients. In particular, we have compared the results of the proposed nonrigid registration algorithm to those obtained using rigid and affine registration techniques. The results clearly indicate that the nonrigid registration algorithm is much better able to recover the motion and deformation of the breast than rigid or affine registration algorithms.},
	Author = {D Rueckert and LI Sonoda and C Hayes and DL Hill and MO Leach and DJ Hawkes},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Breast, Female, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Research Support, Non-U.S. Gov't, 10534053},
	Month = {Aug},
	Number = {8},
	Owner = {tustison},
	Pages = {712-21},
	Title = {Nonrigid registration using free-form deformations: application to breast {MR} images.},
	Volume = {18},
	Year = {1999}}

@inproceedings{Rusinkiewicz2001,
	Author = {Szymon Rusinkiewicz and Marc Levoy},
	Booktitle = {Proceedings of the Third International Conference on 3D Digital Imaging and Modeling},
	Timestamp = {2008.09.02},
	Title = {Efficient Variants of the {ICP} Algorithms},
	Year = {2001}}

@article{Rvachev1995,
	Author = {V. L. Rvachev and T. I. Sheiko},
	Journal = {Applied Mechanics Review},
	Number = {4},
	Owner = {tustison},
	Pages = {151-188},
	Title = {R-functions in boundary value problems in mechanics},
	Volume = {48},
	Year = {1995}}

@article{Saba2003,
	Author = {Osama I Saba and Eric A Hoffman and Joseph M Reinhardt},
	Journal = {J Appl Physiol},
	Month = {Sep},
	Number = {3},
	Pages = {1063--1075},
	Timestamp = {2009.05.18},
	Title = {Maximizing quantitative accuracy of lung airway lumen and wall measures obtained from {X}-ray {CT} imaging.},
	Volume = {95},
	Year = {2003}}

@phdthesis{Sabin1997,
	Author = {Malcolm Arthur Sabin},
	Month = {September},
	Owner = {tustison},
	School = {Leeds University},
	Title = {Spline Finite Elements},
	Year = {1997}}

@article{Samee2003,
	Abstract = {BACKGROUND: Imaging of gas distribution in the lungs of patients with asthma has been restricted because of the lack of a suitable gaseous contrast agent. Hyperpolarized helium-3 (HHe3) provides a new technique for magnetic resonance imaging of lung diseases. OBJECTIVE: We sought to investigate the use of HHe3 gas to image the lungs of patients with moderate or severe asthma and to assess changes in gas distribution after methacholine and exercise challenge. METHODS: Magnetic resonance imaging was performed in asthmatic patients immediately after inhalation of HHe3 gas. In addition, images were obtained before and after methacholine challenge and a standard exercise test. RESULTS: Areas of the lung with no signal or sharply reduced HHe3 signal (ventilation defects) are common in patients with asthma, and the number of defects was inversely related to the percent predicted FEV(1) (r = 0.71, P <.002). After methacholine challenge (n = 3), the number of defects increased. Similarly, imaging of the lungs after exercise (n = 6) showed increased ventilation defects in parallel with decreases in FEV(1). The increase in defects after challenge in these 9 asthmatic patients was significant both for the number (P <.02) and extent (P <.02) of the defects. The variability and speed of changes in ventilation and the complete lack of signal in many areas is in keeping with a model in which the defects result from airway closure. CONCLUSION: HHe3 magnetic resonance provides a new technique for imaging the distribution of inhaled air in the lungs. The technique is suitable for following responses to treatment of asthma and changes after methacholine or exercise challenge.},
	Author = {Saba Samee and Talissa Altes and Patrick Powers and Eduard E de Lange and Jack Knight-Scott and Gary Rakes and John P Mugler and Jonathan M Ciambotti and Bennet A Alford and James R Brookeman and Thomas A E Platts-Mills},
	Journal = {J Allergy Clin Immunol},
	Keywords = {Adolescent; Adult; Asthma; Bronchoconstrictor Agents; Exercise Test; Helium; Humans; Lung; Magnetic Resonance Imaging; Methacholine Chloride},
	Month = {Jun},
	Number = {6},
	Pages = {1205--1211},
	Pii = {S0091674903012806},
	Pmid = {12789218},
	Timestamp = {2007.06.06},
	Title = {Imaging the lungs in asthmatic patients by using hyperpolarized helium-3 magnetic resonance: assessment of response to methacholine and exercise challenge.},
	Volume = {111},
	Year = {2003}}

@article{Satoh2006,
	Author = {Shiro Satoh and Shinichi Ohdama and Hitoshi Shibuya},
	Journal = {Radiat Med},
	Month = {Jul},
	Number = {6},
	Pages = {415--421},
	Timestamp = {2009.05.18},
	Title = {Sliding thin slab, minimum intensity projection imaging for objective analysis of emphysema.},
	Volume = {24},
	Year = {2006}}

@article{Sayad1998,
	Abstract = {Segmental contractile reserve measured by dobutamine magnetic resonance imaging quantitatively predicts improvement in end-systolic wall thickness after revascularization. Segments with end-systolic wall thickness <7 mm at rest do not demonstrate contractile reserve or improve after revascularization.},
	Author = {D. E. Sayad and D. L. Willett and W. G. Hundley and P. A. Grayburn and R. M. Peshock},
	Journal = {Am J Cardiol},
	Keywords = {Adult; Aged; Cardiotonic Agents; Coronary Disease; Dobutamine; Female; Heart Ventricles; Humans; Magnetic Resonance Imaging, Cine; Male; Middle Aged; Myocardial Revascularization; Myocardium; Predictive Value of Tests},
	Month = {Nov},
	Number = {9},
	Pages = {1149--51, A10},
	Pii = {S0002914998005797},
	Pmid = {9817504},
	Timestamp = {2007.09.09},
	Title = {Dobutamine magnetic resonance imaging with myocardial tagging quantitatively predicts improvement in regional function after revascularization.},
	Volume = {82},
	Year = {1998}}

@article{Schechter2003,
	Author = {Guy Schechter and Frederic Devernay and Eve Cost-Maniere and Arshed Quyyumi and Elliot R. McVeigh},
	Journal = {IEEE Transactions on Medical Imaging},
	Number = {4},
	Owner = {tustison},
	Pages = {493-503},
	Title = {Three-Dimensional Motion Tracking of Coronary Arteries in Biplane Cineangiograms},
	Volume = {22},
	Year = {2003}}

@article{Schleicher2009,
	Abstract = {Results from functional imaging studies are often still interpreted using the classical architectonic brain maps of Brodmann and his successors. One obvious weakness in traditional, architectural mapping is the subjective nature of localizing borders between cortical areas by means of a purely visual, microscopical examination of histological specimens. To overcome this limitation, objective mapping procedures based on quantitative cytoarchitecture have been generated. As a result, new maps for various species including man were established. In our contribution, principles of quantitative cytoarchitecture and algorithm-based cortical mapping are described for a cytoarchitectural parcellation of the human auditory cortex. Defining cortical borders based on quantified changes in cortical lamination is the decisive step towards a novel, highly improved probabilistic brain atlas.},
	Author = {Axel Schleicher and Patricia Morosan and Katrin Amunts and Karl Zilles},
	Doi = {10.1007/s10803-009-0790-8},
	Journal = {J Autism Dev Disord},
	Language = {eng},
	Medline-Pst = {aheadofprint},
	Month = {Jul},
	Owner = {stnava},
	Pmid = {19582566},
	Timestamp = {2009.09.02},
	Title = {Quantitative Architectural Analysis: A New Approach to Cortical Mapping.},
	Url = {http://dx.doi.org/10.1007/s10803-009-0790-8},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/s10803-009-0790-8}}

@article{Schnabel2003,
	Abstract = {This paper presents a novel method for validation of nonrigid medical image registration. This method is based on the simulation of physically plausible, biomechanical tissue deformations using finite-element methods. Applying a range of displacements to finite-element models of different patient anatomies generates model solutions which simulate gold standard deformations. From these solutions, deformed images are generated with a range of deformations typical of those likely to occur in vivo. The registration accuracy with respect to the finite-element simulations is quantified by co-registering the deformed images with the original images and comparing the recovered voxel displacements with the biomechanically simulated ones. The functionality of the validation method is demonstrated for a previously described nonrigid image registration technique based on free-form deformations using B-splines and normalized mutual information as a voxel similarity measure, with an application to contrast-enhanced magnetic resonance mammography image pairs. The exemplar nonrigid registration technique is shown to be of subvoxel accuracy on average for this particular application. The validation method presented here is an important step toward more generic simulations of biomechanically plausible tissue deformations and quantification of tissue motion recovery using nonrigid image registration. It will provide a basis for improving and comparing different nonrigid registration techniques for a diversity of medical applications, such as intrasubject tissue deformation or motion correction in the brain, liver or heart.},
	Author = {Julia A Schnabel and Christine Tanner and Andy D Castellano-Smith and Andreas Degenhard and Martin O Leach and D Rodney Hose and Derek L G Hill and David J Hawkes},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Artifacts, Breast, Breast Neoplasms, Comparative Study, Echo-Planar Imaging, Female, Finite Element Analysis, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Motion, Quality Control, Reproducibility of Results, Research Support, Non-U.S. Gov't, Sensitivity and Specificity, Subtraction Technique, 12716000},
	Month = {Feb},
	Number = {2},
	Owner = {tustison},
	Pages = {238-47},
	Title = {Validation of nonrigid image registration using finite-element methods: application to breast {MR} images.},
	Volume = {22},
	Year = {2003}}

@article{Schoenberg1964,
	Author = {I. J. Schoenberg},
	Journal = {Proc. Nat. Acad. Sci.},
	Pages = {947-950},
	Timestamp = {2006.04.12},
	Title = {Spline functions and the problem of graduation},
	Volume = {52},
	Year = {1964}}

@article{Schoenemann2007,
	Author = {P. Thomas Schoenemann and James Gee and Brian Avants and Ralph L Holloway and Janet Monge and Jason Lewis},
	Journal = {Am J Phys Anthropol},
	Month = {Feb},
	Number = {2},
	Pages = {183--192},
	Timestamp = {2009.05.18},
	Title = {Validation of plaster endocast morphology through {3D} {CT} image analysis.},
	Volume = {132},
	Year = {2007}}

@article{Schomaker2004,
	Author = {Schomaker, L. and Bulacu, M.},
	Doi = {10.1109/TPAMI.2004.18},
	Journal = IEEE_J_PAMI,
	Month = {June},
	Number = {6},
	Pages = {787--798},
	Timestamp = {2008.11.26},
	Title = {Automatic writer identification using connected-component contours and edge-based features of uppercase Western script},
	Volume = {26},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2004.18}}

@article{Schroeder2000,
	Author = {William J. Schroeder and Lisa S. Avila and William Hoffman},
	Journal = {IEEE Computer Graphics and Applications},
	Owner = {tustison},
	Pages = {20-27},
	Title = {Visualizing with VTK: A Tutorial},
	Year = {2000}}

@article{Schwetlick1995,
	Author = {Hubert Schwetlick and Torsten Schutze},
	Journal = {BIT},
	Number = {35},
	Owner = {tustison},
	Pages = {1-23},
	Title = {Least Squares Approximation by Splines with Free Knots},
	Year = {1995}}

@article{Sebe2000,
	Author = {Nicu Sebe and Michael S. Lew and Dionysius P. Hujismans},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {10},
	Owner = {tustison},
	Pages = {1132-1143},
	Title = {Toward Improved Ranking Metrics},
	Volume = {22},
	Year = {2000}}

@article{Sederberg1986,
	Author = {Thomas W. Sederberg and Scott R. Parry},
	Journal = {Computer Graphics},
	Number = {4},
	Owner = {tustison},
	Pages = {151-160},
	Title = {Free-Form Deformation of Solid Geometric Models},
	Volume = {20},
	Year = {1986}}

@article{Segars1999,
	Author = {W. Paul Segars and David S. Lalush and Benjamin M. W. Tsui},
	Journal = {IEEE Transactions on Nuclear Science},
	Number = {3},
	Owner = {tustison},
	Pages = {503-506},
	Title = {A Realistic Spline-Based Dynamic Heart Phantom},
	Volume = {46},
	Year = {1999}}

@article{Seidel1993,
	Author = {Hans-Peter Seidel},
	Journal = {IEEE Computer Graphics \& Applications},
	Number = {1},
	Owner = {tustison},
	Pages = {38-46},
	Title = {An Introduction to Polar Forms},
	Volume = {13},
	Year = {1993}}

@techreport{Shapiro1988,
	Author = {Vadim Shapiro},
	Institution = {Cornell Programmable Automation, Sibley School of Mechanical Engineering},
	Owner = {tustison},
	Title = {Theory of R-functions and Applications: A Primer},
	Year = {1988}}

@article{Shechter2004,
	Author = {Guy Shechter and Cengizhan Ozturk and Jon R. Resar and Elliot R. McVeigh},
	Journal = {IEEE Transactions on Medical Imaging},
	Number = {8},
	Owner = {tustison},
	Pages = {1046-1056},
	Title = {Respiratory Motion of the Heart From Free Breathing Coronary Angiograms},
	Volume = {23},
	Year = {2004}}

@article{Shen2002,
	Author = {Dinggang Shen and Christos Davatzikos},
	Journal = {IEEE Transactions on Medical Imaging},
	Number = {11},
	Owner = {tustison},
	Pages = {1421-1439},
	Title = {HAMMER: Hierarchical Attribute Matching Mechanism for Elastic Registration},
	Volume = {21},
	Year = {2002}}

@article{Shen2000,
	Author = {Dinggang Shen and Christos Davatzikos},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {8},
	Owner = {tustison},
	Pages = {906-913},
	Title = {An Adaptive-Focus Deformable Model Using Statistical and Geometric Information},
	Volume = {22},
	Year = {2000}}

@article{Shen2001,
	Author = {Dinggang Shen and Edward H. Herskovits and Christos Davatzikos},
	Journal = {IEEE Transactions on Medical Imaging},
	Number = {4},
	Owner = {tustison},
	Pages = {257-270},
	Title = {An Adaptive-Focus Statistical Shape Model for Segmentation and Shape Modeling of 3-D Brain Structures},
	Volume = {20},
	Year = {2001}}

@article{Shen2003,
	Author = {Hong Shen and Stewart, C.V. and Roysam, B. and Gang Lin and Tanenbaum, H.L.},
	Doi = {10.1109/TPAMI.2003.1182101},
	Journal = IEEE_J_PAMI,
	Month = {March},
	Number = {3},
	Pages = {379--384},
	Timestamp = {2008.11.26},
	Title = {Frame-rate spatial referencing based on invariant indexing and alignment with application to online retinal image registration},
	Volume = {25},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2003.1182101}}

@unpublished{Shewchuk1994,
	Author = {Jonathan Richard Shewchuk},
	Month = {August},
	Timestamp = {2007.06.14},
	Title = {An Introduction to the Conjugate Gradient Method Without the Agonizing Pain},
	Url = {http://www.cs.cmu.edu/~jrs/jrspapers.html},
	Year = {1994},
	Bdsk-Url-1 = {http://www.cs.cmu.edu/~jrs/jrspapers.html}}

@article{Shi2000,
	Author = {Jianbo Shi and Jitendra Malik},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {8},
	Owner = {tustison},
	Pages = {888-905},
	Title = {Normalized Cuts and Image Segmentation},
	Volume = {22},
	Year = {2000}}

@article{Shotton2008,
	Author = {Shotton, J. and Blake, A. and Cipolla, R.},
	Doi = {10.1109/TPAMI.2007.70772},
	Journal = IEEE_J_PAMI,
	Month = {July},
	Number = {7},
	Pages = {1270--1281},
	Timestamp = {2008.11.26},
	Title = {Multiscale Categorical Object Recognition Using Contour Fragments},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70772}}

@inproceedings{Singh2004,
	Author = {M. Singh and H. Arora and N. Ahuja},
	Booktitle = {Proceedings of the IEEE Computer Vision and Pattern Recognition Workshop},
	Pages = {174-182},
	Timestamp = {2008.09.04},
	Title = {Robust registration and tracking using kernel density correlation},
	Year = {2004}}

@phdthesis{Siqueira2006,
	Author = {Marcelo Siqueira},
	Month = {February},
	School = {University of Pennsylvania},
	Timestamp = {2006.06.19},
	Title = {Mesh Generation From Imaging Data},
	Year = {2006}}

@inproceedings{Siqueira2005,
	Author = {Marcelo Siqueira and Longin Jan Latecki and Jean Gallier},
	Booktitle = {Proceedings of the IS\&T/SPIE Conference on Vision Geometry XIII},
	Owner = {tustison},
	Title = {Making 3D Binary Digital Images Well-Composed},
	Year = {2005}}

@article{Siqueira2008,
	Author = {Marcelo Siqueira and Longin Jan Latecki and Jean Gallier and Nicholas Tustison and James Gee},
	Journal = {Journal of Mathematical Imaging and Vision},
	Month = {March},
	Number = {3},
	Pages = {249-274},
	Timestamp = {2007.09.25},
	Title = {Topological Repairing of 3D Digital Images},
	Volume = {30},
	Year = {2008}}

@article{Sled1998,
	Abstract = {A novel approach to correcting for intensity nonuniformity in magnetic resonance (MR) data is described that achieves high performance without requiring a model of the tissue classes present. The method has the advantage that it can be applied at an early stage in an automated data analysis, before a tissue model is available. Described as nonparametric nonuniform intensity normalization (N3), the method is independent of pulse sequence and insensitive to pathological data that might otherwise violate model assumptions. To eliminate the dependence of the field estimate on anatomy, an iterative approach is employed to estimate both the multiplicative bias field and the distribution of the true tissue intensities. The performance of this method is evaluated using both real and simulated MR data.},
	Author = {J. G. Sled and A. P. Zijdenbos and A. C. Evans},
	Doi = {10.1109/42.668698},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Brain; Humans; Magnet; Models, Theoretical; ic Resonance Imaging},
	Month = {Feb},
	Number = {1},
	Pages = {87--97},
	Pmid = {9617910},
	Timestamp = {2009.04.29},
	Title = {A nonparametric method for automatic correction of intensity nonuniformity in MRI data.},
	Url = {http://dx.doi.org/10.1109/42.668698},
	Volume = {17},
	Year = {1998},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/42.668698}}

@article{Sluimer2005,
	Author = {Ingrid Sluimer and Mathias Prokop and Bram van Ginneken},
	Journal = {IEEE Trans Med Imaging},
	Month = {Aug},
	Number = {8},
	Pages = {1025--1038},
	Timestamp = {2009.05.18},
	Title = {Toward automated segmentation of the pathological lung in {CT}.},
	Volume = {24},
	Year = {2005}}

@article{Smith2008,
	Author = {Smith, K. and Ba, S.O. and Odobez, J.-M. and Gatica-Perez, D.},
	Doi = {10.1109/TPAMI.2007.70773},
	Journal = IEEE_J_PAMI,
	Month = {July},
	Number = {7},
	Pages = {1212--1229},
	Timestamp = {2008.11.26},
	Title = {Tracking the Visual Focus of Attention for a Varying Number of Wandering People},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70773}}

@article{Smith2004,
	Author = {Smith, P. and Drummond, T. and Cipolla, R.},
	Doi = {10.1109/TPAMI.2004.1265863},
	Journal = IEEE_J_PAMI,
	Month = {April},
	Number = {4},
	Pages = {479--494},
	Timestamp = {2008.11.26},
	Title = {Layered motion segmentation and depth ordering by tracking edges},
	Volume = {26},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2004.1265863}}

@article{Soille2008,
	Author = {Soille, P.},
	Doi = {10.1109/TPAMI.2007.70817},
	Journal = IEEE_J_PAMI,
	Month = {July},
	Number = {7},
	Pages = {1132--1145},
	Timestamp = {2008.11.26},
	Title = {Constrained Connectivity for Hierarchical Image Decomposition and Simplification},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70817}}

@inproceedings{Song2007,
	Author = {Gang Song and Brian Avants and James Gee},
	Booktitle = {Proceedings of the Workshop on Mathematical Methods in Biomedical Image Analysis},
	Timestamp = {2008.10.29},
	Title = {Multi-start method with prior learning for image registration},
	Year = {2007}}

@inproceedings{Song2009,
	Author = {G. Song and E. Barbosa Jr. and N. J. Tustison and J. C. Gee and W. B. Gefter and M. Kreider and D. A. Torigian},
	Booktitle = {Proceedings of the Intenrational Symposium on Bioemdical Imaging: From Nano to Macro},
	Timestamp = {2009.05.17},
	Title = {COMPUTATIONAL ANALYSIS OF HRCT IMAGES FOR CHARACTERIZATION AND DIFFERENTIATION OF ILD AND COPD},
	Year = {2009}}

@inproceedings{Song2008,
	Author = {Gang Song and Alonso Ramirez-Manzanares and James C. Gee},
	Booktitle = {First International Workshop on Pulmonary Image Analysis in MICCAI 2008},
	Timestamp = {2008.10.22},
	Title = {A Simultaneous Segmentation and Regularization Framework for Vessel Extraction in {CT} Images},
	Year = {2008}}

@inproceedings{Song2006a,
	Author = {Song, Zhuang and Song, Zhuang and Tustison, N. and Avants, B. and Gee, J.},
	Booktitle = {Proc. 3rd IEEE International Symposium on Biomedical Imaging: Nano to Macro},
	Doi = {10.1109/ISBI.2006.1625028},
	Editor = {Tustison, N.},
	Keywords = {Markov processes, biological tissues, biomedical MRI, brain, image registration, image segmentation, iterative methods, medical image processing, optimisation, paediatrics, Markov random field, adaptive graph cuts, atlas-based registration, automatic brain MRI tissue segmentation, inhomogeneity correction, intensity inhomogeneities, iterative algorithm, multispectral image segmentation, neonatal brain MR images, optimization},
	Pages = {762--765},
	Timestamp = {2008.02.10},
	Title = {Adaptive graph cuts with tissue priors for brain MRI segmentation},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/ISBI.2006.1625028}}

@inproceedings{Song2006b,
	Author = {Song, Zhuang and Song, Zhuang and Tustison, N. and Avants, B. and Gee, J.},
	Booktitle = {Proc. of the 3rd International Symposium on Biomedical Imaging: Nano to Macro},
	Editor = {Tustison, N.},
	Pages = {762--765},
	Timestamp = {2009.05.18},
	Title = {Adaptive graph cuts with tissue priors for brain {MRI} segmentation},
	Year = {2006}}

@conference{Song2006,
	Author = {Zhuang Song and Nicholas J. Tustison and Brian B. Avants and James C. Gee},
	Booktitle = {Proc. of the International Symposium on Biomedical Imaging},
	Timestamp = {2006.04.17},
	Title = {Adaptive graph cuts with tissue priors for brain {MRI} segmentation},
	Year = {2006}}

@article{Sorzano2005,
	Abstract = {We present an elastic registration algorithm for the alignment of biological images. Our method combines and extends some of the best techniques available in the context of medical imaging. We express the deformation field as a B-spline model, which allows us to deal with a rich variety of deformations. We solve the registration problem by minimizing a pixelwise mean-square distance measure between the target image and the warped source. The problem is further constrained by way of a vector-spline regularization which provides some control over two independent quantities that are intrinsic to the deformation: its divergence, and its curl. Our algorithm is also able to handle soft landmark constraints, which is particularly useful when parts of the images contain very little information or when its repartition is uneven. We provide an optimal analytical solution in the case when only landmarks and smoothness considerations are taken into account. We have applied our approach to perform the elastic registration of images such as electrophoretic gels and fly embryos. The validation of the results by experts has been favorable in all cases.},
	Journal = {IEEE Trans Biomed Eng},
	Keywords = {Algorithms, Artificial Intelligence, Cluster Analysis, Comparative Study, Elasticity, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Information Storage and Retrieval, Numerical Analysis, Computer-Assisted, Pattern Recognition, Automated, Reproducibility of Results, Research Support, Non-U.S. Gov't, Sensitivity and Specificity, Signal Processing, Computer-Assisted, Subtraction Technique, 15825867},
	Month = {Apr},
	Number = {4},
	Owner = {tustison},
	Pages = {652-63},
	Title = {Elastic registration of biological images using vector-spline regularization.},
	Volume = {52},
	Year = {2005}}

@article{Soundararajan2003,
	Author = {Padmanabhan Soundararajan and Sudeep Sarkar},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {6},
	Owner = {tustison},
	Pages = {642-660},
	Title = {An In-Depth Study of Graph Partitioning Measures for Perceptual Organization},
	Volume = {25},
	Year = {2003}}

@article{Spector2004,
	Abstract = {RATIONALE AND OBJECTIVES: The aim of this study was to establish a standardized procedure for the measurement of regional fractional ventilation in a healthy rat model as a baseline for further studies of pulmonary disorder models. MATERIALS AND METHODS: The lungs of five healthy male Sprague-Dawley rats were imaged using hyperpolarized helium-3 magnetic resonance imaging. From these images, regional fractional ventilation was calculated and maps generated detailing the distribution of fractional ventilation in the lung. The 1.56 mm x 1.56 mm x 4 mm regions of interest were assigned on 5 cm x 5 cm field of view lung maps. Histograms were also generated showing the frequency distribution of fractional ventilation values. To compare fractional ventilation values between animals, the ventilation procedure was standardized to results from individual pulmonary function tests. Each animal's spontaneous tidal volume, respiratory rate, and inspiration percentage (percent of total respiratory cycle in inspiration) were used in their mechanical ventilation settings. RESULTS: Results were similar among all five healthy rats based on examination of ventilation distribution maps and frequency distribution histograms. Mean (0.13) and standard deviation (0.07) were calculated for fractional ventilation in each animal. However, these values were determined to be influenced by slice selection, and therefore the maps and histograms were favored in analysis of results. CONCLUSION: This study shows consistent results in healthy rat lungs and will serve as a baseline study for future measurements in emphysematous rat lungs.},
	Author = {Z. Z. Spector and K. Emami and M. C. Fischer and J. Zhu and M. Ishii and J. Yu and S. Kadlecek and B. Driehuys and R. A. Panettieri and D. A. Lipson and W. Gefter and J. Shrager and R. R. Rizi},
	Doi = {10.1016/j.acra.2004.08.001},
	Institution = {Department of Radiology, University of Pennsylvania School of Medicine, Stellar-Chance Laboratories, 422 Curie Boulevard, Philadelphia, PA 19104, USA.},
	Journal = {Acad Radiol},
	Keywords = {Animals; Helium; Isotopes; Magnetic Resonance Imaging; Male; Models, Animal; Pulmonar; Pulmonary Ventilation; Rats; Rats, Sprague-Dawley; y Alveoli},
	Month = {Oct},
	Number = {10},
	Pages = {1171--1179},
	Pii = {S1076-6332(04)00433-7},
	Pmid = {15530811},
	Timestamp = {2008.01.10},
	Title = {A small animal model of regional alveolar ventilation using HP 3He MRI1.},
	Url = {http://dx.doi.org/10.1016/j.acra.2004.08.001},
	Volume = {11},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.acra.2004.08.001}}

@article{Srivastava2005,
	Author = {Anuj Srivastava and Shantanu H. Joshi and Washington Mio and Xiuwen Liu},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {4},
	Owner = {tustison},
	Pages = {590-602},
	Title = {Statistical Shape Analysis: Clustering Learning and Testing},
	Volume = {27},
	Year = {2005}}

@article{Staring2007,
	Author = {Marius Staring and Stefan Klein and Josien P.W. Pluim},
	Journal = {Medical Physics},
	Pages = {4098-4108},
	Timestamp = {2008.10.02},
	Title = {A Rigidity Penalty Term for Nonrigid Registration},
	Volume = {34},
	Year = {2007}}

@inproceedings{Staring2006,
	Author = {Marius Staring and Stefan Klein and Josien P. W. Pluim},
	Booktitle = {Proceedings of the SPIE: Medical Imaging},
	Timestamp = {2006.06.19},
	Title = {Nonrigid Registration Using a Rigidity Constraint},
	Volume = {6144},
	Year = {2006}}

@article{Stavngaard2006,
	Author = {T. Stavngaard and S. B. Shaker and K. S. Bach and B. C. Stoel and A. Dirksen},
	Journal = {Acta Radiol},
	Month = {Nov},
	Number = {9},
	Pages = {914--921},
	Timestamp = {2009.05.18},
	Title = {Quantitative assessment of regional emphysema distribution in patients with chronic obstructive pulmonary disease (COPD).},
	Volume = {47},
	Year = {2006}}

@article{Steinwart2003,
	Author = {Steinwart, I.},
	Doi = {10.1109/TPAMI.2003.1233901},
	Journal = IEEE_J_PAMI,
	Month = {Oct.},
	Number = {10},
	Pages = {1274--1284},
	Timestamp = {2008.11.26},
	Title = {On the optimal parameter choice for \&support vector machines},
	Volume = {25},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2003.1233901}}

@article{Stoel2004,
	Author = {Berend C Stoel and Jan Stolk},
	Journal = {Invest Radiol},
	Month = {Nov},
	Number = {11},
	Pages = {681--688},
	Timestamp = {2009.05.18},
	Title = {Optimization and standardization of lung densitometry in the assessment of pulmonary emphysema.},
	Volume = {39},
	Year = {2004}}

@article{Stolk2001,
	Author = {J. Stolk and A. Dirksen and A. A. van der Lugt and J. Hutsebaut and J. Mathieu and J. de Ree and J. H. Reiber and B. C. Stoel},
	Journal = {Invest Radiol},
	Month = {Nov},
	Number = {11},
	Pages = {648--651},
	Timestamp = {2009.05.18},
	Title = {Repeatability of lung density measurements with low-dose computed tomography in subjects with alpha-1-antitrypsin deficiency-associated emphysema.},
	Volume = {36},
	Year = {2001}}

@article{Stolk2007,
	Author = {Jan Stolk and Hein Putter and Els M Bakker and Saher B Shaker and David G Parr and Eeva Piitulainen and Erich W Russi and Elzbieta Grebski and Asger Dirksen and Robert A Stockley and Johan H C Reiber and Berend C Stoel},
	Journal = {Respir Med},
	Month = {Sep},
	Number = {9},
	Pages = {1924--1930},
	Timestamp = {2009.05.18},
	Title = {Progression parameters for emphysema: a clinical investigation.},
	Volume = {101},
	Year = {2007}}

@article{Strange2007,
	Author = {Charlie Strange and Felix J F Herth and Kevin L Kovitz and Geoffrey McLennan and Armin Ernst and Jonathan Goldin and Marc Noppen and Gerard J Criner and Frank C Sciurba and V. E. N. T. Study Group},
	Journal = {BMC Pulm Med},
	Pages = {10},
	Timestamp = {2009.05.18},
	Title = {Design of the Endobronchial Valve for Emphysema Palliation Trial (VENT): a non-surgical method of lung volume reduction.},
	Volume = {7},
	Year = {2007}}

@article{Strek2006,
	Abstract = {The correct diagnosis of asthma is usually easily made and most patients with asthma respond to therapy. Approximately 5\% of patients with asthma, however, have disease that is difficult to control despite taking maximal doses of inhaled medications. Patients with therapy-resistant or difficult-to-control asthma require a rigorous and systematic approach to their diagnosis and treatment. The first step is evaluation and testing directed at determining that asthma is the correct diagnosis. Many diseases mimic asthma and these alternate diagnoses should be considered. The second step is to identify and eliminate triggers that worsen asthma. Cigarette smoking, occupational exposures, and allergic rhinitis contribute to worsening disease. Most patients with "difficult asthma" require treatment with high-dose inhaled corticosteroids and long-acting inhaled beta(2)-agonists. Despite maximal inhaled therapy, these patients will require either frequent bursts or chronic daily therapy with oral corticosteroids. These patients may have "resistant" inflammation with a persistent inflammatory state. Numerous studies also suggest that compliance with asthma therapy is poor. Combination therapy with inhaled corticosteroids and long-acting beta(2)-agonist in a single inhaler may improve patient compliance. In selected patients, additional therapy with leukotriene modifiers or anti-IgE antibody can result in improved asthma control and may allow tapering of corticosteroids. Use of methotrexate is not justified based on current data. Emerging evidence suggests that different phenotypes of difficult or therapy-resistant asthma exist. Recognition of these subgroups allows tailored therapy and prevents overmedication in an attempt to normalize lung function in patients with irreversible airflow obstruction.},
	Author = {Mary E Strek},
	Doi = {10.1513/pats.200510-115JH},
	Journal = {Proc Am Thorac Soc},
	Keywords = {Asthma; Bronchodilator Agents; Diagnosis, Differential; Glucocorticoids; Humans; Prognosis; Severity of Illness Index},
	Number = {1},
	Pages = {116--123},
	Pii = {3/1/116},
	Pmid = {16493159},
	Timestamp = {2007.09.08},
	Title = {Difficult asthma.},
	Url = {http://dx.doi.org/10.1513/pats.200510-115JH},
	Volume = {3},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1513/pats.200510-115JH}}

@article{Studholme1997,
	Author = {Colin Studholme and Derek L. G. Hill and David J. Hawkes},
	Journal = {Medical Physics},
	Number = {1},
	Owner = {tustison},
	Pages = {25-35},
	Title = {Automated three-dimensional registration of magnetic resonance and positron emission tomography brain images by multiresolution optimization of voxel similarity measures},
	Volume = {24},
	Year = {1997}}

@article{Styner2000,
	Abstract = {This paper presents a new approach to the correction of intensity inhomogeneities in magnetic resonance imaging (MRI) that significantly improves intensity-based tissue segmentation. The distortion of the image brightness values by a low-frequency bias field impedes visual inspection and segmentation. The new correction method called parametric bias field correction (PABIC) is based on a simplified model of the imaging process, a parametric model of tissue class statistics, and a polynomial model of the inhomogeneity field. We assume that the image is composed of pixels assigned to a small number of categories with a priori known statistics. Further we assume that the image is corrupted by noise and a low-frequency inhomogeneity field. The estimation of the parametric bias field is formulated as a nonlinear energy minimization problem using an evolution strategy (ES). The resulting bias field is independent of the image region configurations and thus overcomes limitations of methods based on homomorphic filtering. Furthermore, PABIC can correct bias distortions much larger than the image contrast. Input parameters are the intensity statistics of the classes and the degree of the polynomial function. The polynomial approach combines bias correction with histogram adjustment, making it well suited for normalizing the intensity histogram of datasets from serial studies. We present simulations and a quantitative validation with phantom and test images. A large number of MR image data acquired with breast, surface, and head coils, both in two dimensions and three dimensions, have been processed and demonstrate the versatility and robustness of this new bias correction scheme.},
	Doi = {10.1109/42.845174},
	Institution = {Department of Computer Science, University of North Carolina at Chapel Hill, 27514, USA. martin_styner@ieee.org},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Brain; Breast; Female; Humans; Image Processing, Computer-Assisted; Magnetic Resonance Imaging; Models, Theoretical; Phantoms, Imaging; Reproducibility of Results},
	Month = {Mar},
	Number = {3},
	Pages = {153--165},
	Pmid = {10875700},
	Timestamp = {2009.04.29},
	Title = {Parametric estimate of intensity inhomogeneities applied to MRI.},
	Url = {http://dx.doi.org/10.1109/42.845174},
	Volume = {19},
	Year = {2000},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/42.845174}}

@article{Suga1999,
	Abstract = {To evaluate impaired respiratory mechanics in pulmonary emphysema, dynamic breathing magnetic resonance imaging (BMRI) was acquired with fast-gradient echo pulse sequences at fixed thoracic planes over two to three slow, deep respiratory cycles in 6 controls and 28 patients with pulmonary emphysema including 9 patients undergoing lung volume reduction surgery (LVRS). Respiratory motions of the diaphragm and chest wall (D/CW) were assessed by a cine-loop view, a fusion display of maximal inspiratory and expiratory images, and the time-distance curves. By contrast with normal subjects with regular synchronous D/CW motions, the patients frequently showed reduced, irregular, or asynchronous motions, with significant decreases in the maximal amplitude of D/CW motions (MAD and MACW), and the length of apposition of the diaphragm (LAD) (P < 0.0001, P < 0.001, P < 0. 01, respectively). After LVRS, nine patients showed improvements in D/CW configuration and mobility, with significantly increased MAD, MACW, and LAD (P < 0.01, P < 0.0001, and P < 0.05, respectively). In 40 studies of 28 patients including the post-LVRS examinations, the normalized MAD and MACW significantly correlated with \%FEV(1) (r = 0. 881 and r = 0.906; P < 0.0001, respectively). BMRI seems useful for noninvasively and directly assessing the impaired respiratory mechanics associated with abnormal ventilation in pulmonary emphysema, and also for monitoring the effects of LVRS. J. Magn. Reson. Imaging 1999;10:510-520.},
	Author = {K. Suga and T. Tsukuda and H. Awaya and K. Takano and S. Koike and N. Matsunaga and K. Sugi and K. Esato},
	Institution = {Department of Radiology, Yamaguchi University School of Medicine, Ube, Yamaguchi, Japan.},
	Journal = {J Magn Reson Imaging},
	Keywords = {Aged; Diaphragm; Female; Humans; Magnetic Resonance Imaging; Male; Middle Aged; Movement; Pneumonectomy; Pulmonary Emphysema; Respiratory Mechanics; Respiratory Muscles; Thorax},
	Month = {Oct},
	Number = {4},
	Pages = {510--520},
	Pii = {3.0.CO;2-G},
	Pmid = {10508317},
	Timestamp = {2008.01.24},
	Title = {Impaired respiratory mechanics in pulmonary emphysema: evaluation with dynamic breathing MRI.},
	Volume = {10},
	Year = {1999}}

@article{Sumengen2006,
	Author = {Baris Sumengen and B. S. Manjunath},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {4},
	Owner = {tustison},
	Pages = {509-521},
	Title = {Graph Partitioning Active Contours (GPAC) for Image Segmentation},
	Volume = {28},
	Year = {2006}}

@inproceedings{Sundaram2004,
	Author = {T. A. Sundaram and B. B. Avants and J. C. Gee},
	Booktitle = {Proc. of the 7th International Conference of Medical Image Computing and Computer-Assisted Intervention},
	Editor = {C. Barillot and D. R. Haynor and P. Hellier},
	Month = {September},
	Pages = {1000-1007},
	Publisher = {Springer},
	Series = {Lecture Notes in Computer Science},
	Timestamp = {2009.05.18},
	Title = {A Dynamic Model of Average Lung Deformation Using Capacity-Based Reparameterization and Shape Averaging of Lung {MR} Images},
	Volume = {3217},
	Year = {2004}}

@article{Sundaram2005,
	Author = {Tessa A Sundaram and Brian B Avants and James C Gee},
	Journal = {Med Image Comput Comput Assist Interv Int Conf Med Image Comput Comput Assist Interv},
	Number = {Pt 2},
	Pages = {328--335},
	Timestamp = {2009.05.18},
	Title = {Towards a dynamic model of pulmonary parenchymal deformation: evaluation of methods for temporal reparameterization of lung data.},
	Volume = {8},
	Year = {2005}}

@article{Sundaram2005a,
	Author = {Tessa A Sundaram and James C Gee},
	Journal = {Med Image Anal},
	Month = {Dec},
	Number = {6},
	Pages = {524--537},
	Timestamp = {2009.05.18},
	Title = {Towards a model of lung biomechanics: pulmonary kinematics via registration of serial lung images.},
	Volume = {9},
	Year = {2005}}

@inproceedings{Sundaram2003,
	Author = {T. A. Sundaram and J. C. Gee},
	Booktitle = {Proc. of the 11th Annual Meeting of ISMRM},
	Pages = {410},
	Timestamp = {2009.05.18},
	Title = {Biomechanical analysis of the lung: a feature-based approach using customized finite element meshes},
	Year = {2003}}

@inproceedings{Sundaram2005b,
	Author = {T. A. Sundaram and S. Kubo and H. Hatabu and M. Takahashi and J. C. Gee},
	Booktitle = {Proc. of the 13th Annual Meeting of ISMRM},
	Pages = {in press},
	Timestamp = {2009.05.18},
	Title = {Validation of Shape Averaging for Modeling Average Lung Deformation in {2-D} Ventilator-Acquired Mouse {MR} Sequences},
	Year = {2005}}

@inproceedings{Sundaram2005d,
	Author = {T. A. Sundaram and S. Kubo and A. Kino and H. Hatabu and M. Takahashi and J. C. Gee},
	Booktitle = {Proc. of the 13th Annual Meeting of ISMRM},
	Pages = {in press},
	Timestamp = {2009.05.18},
	Title = {Whole-Lung Parenchymal Dynamics: Evaluation of Motion Estimation Using Non-Rigid Registration},
	Year = {2005}}

@inproceedings{Sundaram2007,
	Author = {T. A. Sundaram and K. Ruppert and A. Hernandez and B. Avants and T. Altes and J.C. Gee},
	Booktitle = {Proc. of the 15th Annual Meeting of ISMRM},
	Pages = {3039},
	Timestamp = {2009.05.18},
	Title = {Quantitative Comparison of Registration-Based Lung Motion Estimates from Whole-Lung {MR} Images and Corresponding Two-Dimensional Slices.},
	Year = {2007}}

@inproceedings{Sundaram2003a,
	Author = {T.A. Sundaram and J.C. Gee},
	Booktitle = {Eastern-Atlantic Student Research Forum},
	Timestamp = {2009.05.18},
	Title = {Using Anatomy-Specific Meshes to Compute Lung Motion from {MR} Images},
	Year = {2003}}

@inproceedings{Sundaram2002,
	Author = {T.A. Sundaram and J.C. Gee and I. Hawegawa and H. Uematsu and H. Hatabu},
	Booktitle = {Proc. of the 10th Annual Meeting of ISMRM},
	Timestamp = {2009.05.18},
	Title = {Validation of a Registration Algorithm for Computing Lung Deformation from {MR} Images},
	Year = {2002}}

@inproceedings{Sundaram2004a,
	Author = {T. Sundaram and J. Gee and M. Nishino and S. Kiryu and Y. Mori and M. Kuroki and M. Takahashi and H. Hatabu},
	Booktitle = {Proc. of the 12th Annual Meeting of ISMRM},
	Pages = {2609},
	Timestamp = {2009.05.18},
	Title = {{3-D} Lung Motion Estimation Via Non-Rigid Registration Using Volumetric {MR} and {CT}},
	Year = {2004}}

@inproceedings{Sundaram2007a,
	Author = {T.A. Sundaram and S. Kubo and T. Kubo and M. Takahashi H. Hatabu and J.C. Gee},
	Booktitle = {Proc. of the 15th Annual Meeting of ISMRM},
	Timestamp = {2009.05.18},
	Title = {Landmark-Based Assessment of Human Lung Motion Analysis via Registration of Sagittal {2-D} {MR} Images},
	Year = {2007}}

@inproceedings{Sundaram2006,
	Author = {T.A. Sundaram and S. Kubo and M. Takahashi and H. Hatabu and J.C. Gee},
	Booktitle = {Proc. of the 14th Annual Meeting of ISMRM},
	Timestamp = {2009.05.18},
	Title = {Towards a normative lung atlas: validation of physiologically appropriate temporal reparameterization of dynamic lung {MR} sequences},
	Year = {2006}}

@article{Sung2008,
	Author = {Sung, Jaemo and Ghahramani, Zoubin and Bang, Sung-Yang},
	Doi = {10.1109/TPAMI.2008.157},
	Journal = IEEE_J_PAMI,
	Month = {Dec.},
	Number = {12},
	Pages = {2236--2242},
	Timestamp = {2008.11.26},
	Title = {Latent-Space Variational Bayes},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2008.157}}

@article{Szeliski1997,
	Author = {Richard Szeliski and James Coughlan},
	Journal = {International Journal of Computer Vision},
	Number = {3},
	Owner = {tustison},
	Pages = {199-218},
	Title = {Spline-Based Image Registration},
	Volume = {22},
	Year = {1997}}

@article{Tajik2002,
	Author = {Jehangir K Tajik and Deokiee Chon and Chulho Won and Binh Q Tran and Eric A Hoffman},
	Journal = {Acad Radiol},
	Month = {Feb},
	Number = {2},
	Pages = {130--146},
	Timestamp = {2009.05.18},
	Title = {Subsecond multisection {CT} of regional pulmonary ventilation.},
	Volume = {9},
	Year = {2002}}

@inproceedings{Takahashi2004,
	Author = {M. Takahashi and S. Kiryu and J. C. Gee and T. A. Sundaram and T. Asakura and H. Hatabu},
	Booktitle = {Proc. of the 2nd International Workshop on Pulmonary Functional Imaging},
	Timestamp = {2009.05.18},
	Title = {Magnetic resonance imaging analysis of regional pulmonary motion of mice: Comparison between wild-type mice and transgenic mice that produce human sickle hemoglobin.},
	Year = {2004}}

@inproceedings{Takahashi2007,
	Author = {M. Takahashi and S. Kubo and T.A. Sundaram and J.C. Gee and H. Hatabu},
	Booktitle = {Proc. of the 15th Annual Meeting of ISMRM},
	Pages = {2768},
	Timestamp = {2009.05.18},
	Title = {Four dimensional {MR} microscopy of respiratory mechanics in transgenic mice with emphysema: Lung motion quantification via a non-rigid registration algorithm},
	Year = {2007}}

@article{Tao2008,
	Author = {Tao, Qingping and Scott, Stephen D. and Vinodchandran, N. V. and Osugi, Thomas Takeo and Mueller, Brandon},
	Doi = {10.1109/TPAMI.2007.70846},
	Journal = IEEE_J_PAMI,
	Month = {Dec.},
	Number = {12},
	Pages = {2084--2098},
	Timestamp = {2008.11.26},
	Title = {Kernels for Generalized Multiple-Instance Learning},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70846}}

@article{Teh1988,
	Author = {Cho-Huak Teh and Roland T. Chin},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {4},
	Owner = {tustison},
	Pages = {496-512},
	Title = {On Image Analysis by the Methods of Moments},
	Volume = {10},
	Year = {1988}}

@article{Temizoz2007,
	Author = {Osman Temizoz and Omer Etlik and Mehmet Emin Sakarya and Kursat Uzun and Halil Arslan and Mustafa Harman and Mustafa Kemal Demir},
	Journal = {Comput Med Imaging Graph},
	Month = {Oct},
	Number = {7},
	Pages = {542--548},
	Timestamp = {2009.05.18},
	Title = {Detection and quantification of the parenchymal abnormalities in emphysema using pulmo-{CT}.},
	Volume = {31},
	Year = {2007}}

@article{Terzopoulos1991,
	Author = {Demetri Terzopoulos and Dimitri Metaxas},
	Journal = {IEEE Transactions on Pattern Analysis And Machine Intelligence},
	Month = {July},
	Number = {7},
	Owner = {tustison},
	Pages = {703-714},
	Title = {Dynamic 3D Models with Local and Global Deformations: Deformable Superquadrics},
	Volume = {13},
	Year = {1991}}

@article{Thevenaz1998,
	Author = {Philippe Thevenaz and Urs E. Ruttimann and Michael Unser},
	Journal = {IEEE Transactions on Image Processing},
	Number = {1},
	Owner = {tustison},
	Pages = {27-41},
	Title = {A Pyramid Approach to Subpixel Registration Based on Intensity},
	Volume = {7},
	Year = {1998}}

@article{Thirion1998,
	Author = {J.-P. Thirion},
	Journal = {Medical Image Analysis},
	Number = {3},
	Owner = {tustison},
	Pages = {243-260},
	Title = {Image matching as a diffusion process: an analogy with {M}axwell's demons},
	Volume = {2},
	Year = {1998}}

@article{Thompson1997,
	Abstract = {This paper describes the design, implementation and preliminary results of a technique for creating a comprehensive probabilistic atlas of the human brain based on high-dimensional vector field transformations. The goal of the atlas is to detect and quantify distributed patterns of deviation from normal anatomy, in a 3-D brain image from any given subject. The algorithm analyzes a reference population of normal scans and automatically generates color-coded probability maps of the anatomy of new subjects. Given a 3-D brain image of a new subject, the algorithm calculates a set of high-dimensional volumetric maps (with typically 384(2) x 256 x 3 approximately 10(8) degrees of freedom) elastically deforming this scan into structural correspondence with other scans, selected one by one from an anatomic image database. The family of volumetric warps thus constructed encodes statistical properties and directional biases of local anatomical variation throughout the architecture of the brain. A probability space of random transformations, based on the theory of anisotropic Gaussian random fields, is then developed to reflect the observed variability in stereotaxic space of the points whose correspondences are found by the warping algorithm. A complete system of 384(2) x 256 probability density functions is computed, yielding confidence limits in stereotaxic space for the location of every point represented in the 3-D image lattice of the new subject's brain. Color-coded probability maps are generated, densely defined throughout the anatomy of the new subject. These indicate locally the probability of each anatomic point being unusually situated, given the distributions of corresponding points in the scans of normal subjects. 3-D MRI and high-resolution cryosection volumes are analyzed from subjects with metastatic tumors and Alzheimer's disease. Gradual variations and continuous deformations of the underlying anatomy are simulated and their dynamic effects on regional probability maps are animated in video format (on the accompanying CD-ROM). Applications of the deformable probabilistic atlas include the transfer of multi-subject 3-D functional, vascular and histologic maps onto a single anatomic template, the mapping of 3-D atlases onto the scans of new subjects, and the rapid detection, quantification and mapping of local shape changes in 3-D medical images in disease and during normal or abnormal growth and development.},
	Author = {PM Thompson and AW Toga},
	Journal = {Med Image Anal},
	Keywords = {Anatomy, Cross-Sectional, Brain, Brain Mapping, Comparative Study, Computer Simulation, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Models, Anatomic, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S., Research Support, U.S. Gov't, P.H.S., 9873911},
	Month = {Sep},
	Number = {4},
	Owner = {tustison},
	Pages = {271-94},
	Pii = {S1361841597850025},
	Title = {Detection, visualization and animation of abnormal anatomic structure with a deformable probabilistic brain atlas based on random vector field transformations.},
	Volume = {1},
	Year = {1997}}

@article{Thurlbeck1994,
	Journal = {AJR Am J Roentgenol},
	Month = {Nov},
	Number = {5},
	Pages = {1017--1025},
	Timestamp = {2009.05.18},
	Title = {Emphysema: definition, imaging, and quantification.},
	Volume = {163},
	Year = {1994}}

@article{Todorovic2008,
	Author = {Todorovic, Sinisa and Ahuja, Narendra},
	Doi = {10.1109/TPAMI.2008.24},
	Journal = IEEE_J_PAMI,
	Month = {Dec.},
	Number = {12},
	Pages = {2158--2174},
	Timestamp = {2008.11.26},
	Title = {Unsupervised Category Modeling, Recognition, and Segmentation in Images},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2008.24}}

@article{Torigian2007,
	Author = {Drew A Torigian and Warren B Gefter and John D Affuso and Kiarash Emami and Lawrence Dougherty},
	Journal = {AJR Am J Roentgenol},
	Month = {Mar},
	Number = {3},
	Pages = {W276--W280},
	Timestamp = {2009.05.18},
	Title = {Application of an optical flow method to inspiratory and expiratory lung {MDCT} to assess regional air trapping: a feasibility study.},
	Volume = {188},
	Year = {2007}}

@article{Trouve1998,
	Author = {Alain Trouve},
	Journal = {International Journal of Computer Vision},
	Number = {3},
	Owner = {tustison},
	Pages = {213-221},
	Title = {Diffeomorphisms Groups and Pattern Matching in Image Analysis},
	Volume = {28},
	Year = {1998}}

@techreport{Trouve1995,
	Author = {Alain Trouve},
	Institution = {Center for Imaging Science, Johns Hopkins University},
	Owner = {tustison},
	Title = {An Infinite DImensional Group Approach For Physics Based Models in Patterns Recognition},
	Year = {1995}}

@article{Tsallis1988,
	Author = {C. Tsallis},
	Journal = {Journal of Statistical Physics},
	Pages = {479-487},
	Timestamp = {2008.09.04},
	Title = {Possible generalization of {B}oltzmann-{G}ibbs statistics},
	Volume = {52},
	Year = {1988}}

@article{Tschirren2005,
	Author = {Juerg Tschirren and Eric A Hoffman and Geoffrey McLennan and Milan Sonka},
	Journal = {IEEE Trans Med Imaging},
	Month = {Dec},
	Number = {12},
	Pages = {1529--1539},
	Timestamp = {2009.05.18},
	Title = {Intrathoracic airway trees: segmentation and airway morphology analysis from low-dose {CT} scans.},
	Volume = {24},
	Year = {2005}}

@article{Tschirren2005a,
	Journal = {IEEE Trans Med Imaging},
	Month = {Dec},
	Number = {12},
	Pages = {1540--1547},
	Timestamp = {2009.05.18},
	Title = {Matching and anatomical labeling of human airway tree.},
	Volume = {24},
	Year = {2005}}

@inproceedings{Tsin2004,
	Author = {Y. Tsin and T. Kanade},
	Booktitle = {Proceedings of the European Conference on Computer Vision},
	Pages = {558-569},
	Timestamp = {2008.09.04},
	Title = {A correlation based approach for robust point-set registration},
	Year = {2004}}

@article{Tsukanov2003,
	Author = {I. Tsukanov and M. Hall},
	Journal = {International Journal for Numerical Methods in Engineering},
	Owner = {tustison},
	Pages = {1949-1972},
	Title = {Data structure and algorithms for fast automatic differentiation},
	Volume = {56},
	Year = {2003}}

@article{Turner1986,
	Author = {M. R. Turner},
	Journal = {Biological Cybernetics},
	Pages = {71-82},
	Timestamp = {2007.12.13},
	Title = {Texture discrimination by {G}abor functions},
	Volume = {55},
	Year = {1986}}

@inproceedings{Tustison2007h,
	Author = {Tustison, N.J. and Altes, T.A. and Gee, J.C. and Cai, J. and de Lange, E.E. and Mugler, J.P.},
	Booktitle = {Proc. 4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro ISBI 2007},
	Doi = {10.1109/ISBI.2007.356865},
	Editor = {Altes, T.A.},
	Keywords = {biomechanics, biomedical MRI, deformation, helium, lung, splines (mathematics), B-spline approximation algorithm, cardiac research, deformation field interpolation, high contrast tag lines, hyperpolarized helium-3, lung displacement, lung kinematic information, lung strain, magnetic resonance tagging techniques, myocardial deformation, pulmonary deformation, pulmonary kinematics, sparse tag line, tagged magnetic resonance imaging},
	Pages = {368--371},
	Timestamp = {2008.02.10},
	Title = {PULMONARY KINEMATICS FROM HYPERPOLARIZED HELIUM-3 TAGGED MAGNETIC RESONANCE IMAGING},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/ISBI.2007.356865}}

@inproceedings{Tustison2002a,
	Author = {Tustison, N.J. and Amini, A.A.},
	Booktitle = {Proc. Second Joint [Engineering in Medicine and Biology 24th Annual Conference and the Annual Fall Meeting of the Biomedical Engineering Society] EMBS/BMES Conference},
	Doi = {10.1109/IEMBS.2002.1106242},
	Editor = {Amini, A.A.},
	Issn = {1094-687X},
	Keywords = {biomechanics, biomedical MRI, cardiology, image motion analysis, medical image processing, modelling, muscle, splines (mathematics), tracking, 4-D B-spline model, SPAMM-MRI, cardiac motion simulator, in-vivo pig data, knot planes, magnetic resonance imaging, medical diagnostic imaging, movie loop, myocardial beads tracking, nonrigid movement visualization, simulated data, spatio-temporal internal energy},
	Pages = {993--994 vol.2},
	Timestamp = {2008.02.10},
	Title = {Tracking myocardial beads from SPAMM-MRI with a 4-D B-spline model},
	Volume = {2},
	Year = {2002},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/IEMBS.2002.1106242}}

@inproceedings{Tustison2008d,
	Author = {NJ Tustison and CJ Kotzer and GA Logan and PL Podolin and TA Altes and AP Wright and G Song and H Zhao and A Haczku and MS Barnette and RA Panettieri and JC Gee},
	Booktitle = {Proceedings of the American Thoracic Society},
	Timestamp = {2009.03.16},
	Title = {Detection of elastase induced emphysema in free-breathing mice using micro computed tomography (CT)},
	Year = {2008}}

@inproceedings{Tustison2004b,
	Author = {Tustison, N.J. and Tustison, N.J. and Abendschein, D. and Amini, A.A.},
	Booktitle = {Proc. IEEE Computer Society Conference on Computer Vision and Pattern Recognition CVPR 2004},
	Doi = {10.1109/CVPR.2004.1315207},
	Editor = {Abendschein, D.},
	Issn = {1063-6919},
	Keywords = {biomedical MRI, biomedical measurement, blood vessels, cardiovascular system, haemodynamics, quadratic programming, anatomical NURBS models, biventricular myocardial kinematics, nonuniform rational D-splines, quadratic programming, tagged MRI, ventricular deformation, volumetric deformable models},
	Pages = {II-514--II-519 Vol.2},
	Timestamp = {2008.02.10},
	Title = {Biventricular myocardial kinematics based on tagged MRI from anatomical NURBS models},
	Volume = {2},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/CVPR.2004.1315207}}

@inproceedings{Tustison2002b,
	Author = {Tustison, N.J. and Tustison, N.J. and Abendschein, D. and Davila-Roman, V.G. and Amini, A.A.},
	Booktitle = {Proc. 16th International Conference on Pattern Recognition},
	Doi = {10.1109/ICPR.2002.1044860},
	Editor = {Abendschein, D.},
	Issn = {1051-4651},
	Keywords = {biomedical MRI, cardiology, medical image processing, splines (mathematics), displacement field reconstruction, dynamic motion, heartfrom, long axis Lagrangian strain maps, myocardial deformation, short axis Lagrangian strain maps, spatiotemporal internal energy, tagged magnetic resonance imaging},
	Pages = {723--726 vol.1},
	Timestamp = {2008.02.10},
	Title = {Myocardial strain imaging with tagged MRI},
	Volume = {1},
	Year = {2002},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/ICPR.2002.1044860}}

@article{Tustison2006d,
	Author = {Tustison, N.J. and Tustison, N.J. and Amini, A.A.},
	Doi = {10.1109/TMI.2005.861015},
	Editor = {Amini, A.A.},
	Issn = {0278-0062},
	Journal = IEEE_J_MI,
	Keywords = {biomechanics, biomedical MRI, cardiology, deformation, image registration, medical image processing, splines (mathematics), AnFigatomical NURBS Models, Cartesian NURBS models, Eulerian strain maps, Lagrangian maps, biventricular myocardial strains, end-diastole, endocardial contours, epicardial contours, nonrigid image registration, nonuniform rational B-splines, quadratic programming, tagged cardiac magnetic resonance imaging, ventricle, ventricular deformation, volumetric deformable models, weighted least squares, B-splines, NURBS, cardiac motion, deformation, myocardial strain, nonrigid registration, tagged MRI},
	Number = {1},
	Pages = {94--112},
	Timestamp = {2008.02.10},
	Title = {Biventricular myocardial strains via nonrigid registration of AnFigatomical NURBS models},
	Volume = {25},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TMI.2005.861015}}

@article{Tustison2003a,
	Author = {Tustison, N.J. and Tustison, N.J. and Davila-Roman, V.G. and Amini, A.A.},
	Doi = {10.1109/TBME.2003.814530},
	Editor = {Davila-Roman, V.G.},
	Issn = {0018-9294},
	Journal = IEEE_J_BME,
	Keywords = {biomechanics, biomedical MRI, cardiology, image coding, kinematics, muscle, physiological models, splines (mathematics), 3-D intersections, 4-D B-spline model, functional imaging method, left ventricular dynamics modeling, magnetic resonance imaging, medical diagnostic imaging, movie loop, myocardial beads, myocardial kinematics, nonrigid movement visualization, orthogonal tag planes triplets, signal voids grid encoding, spatio-temporal internal energy, tagged MRI},
	Number = {8},
	Pages = {1038--1040},
	Timestamp = {2008.02.10},
	Title = {Myocardial kinematics from tagged MRI based on a 4-D B-spline model},
	Volume = {50},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TBME.2003.814530}}

@inproceedings{Tustison2004,
	Author = {N. J. Tustison and D. Abendschein and A. A. Amini},
	Booktitle = {IEEE Computer Society Conference on Computer Vision and Pattern Recognition},
	Journal = {IEEE Computer Society Conference on Computer Vision and Pattern Recognition},
	Month = {June},
	Pages = {514},
	Timestamp = {2007.09.25},
	Title = {Biventricular Myocardial Kinematics Based on Tagged MRI from Anatomical NURBS Models},
	Volume = {2},
	Year = {2004}}

@inproceedings{Tustison2002,
	Author = {N. J. Tustison and D. Abendschein and V. G. Davila-Roman and A. A. Amini},
	Booktitle = {Proceedings of the International Conference on Pattern Recognition},
	Month = {August},
	Pages = {723-726},
	Timestamp = {2007.09.25},
	Title = {Myocardial Strain Imaging with Tagged MRI},
	Volume = {1},
	Year = {2002}}

@inproceedings{Tustison2007a,
	Author = {Nicholas J. Tustison and Talissa A. Altes and James C. Gee and Jing Cai and Eduarde E. de Lange and John P. MuglerIII},
	Booktitle = {4th IEEE International Symposium on Biomedical Imaging: From Nano to Macro,},
	Timestamp = {2007.03.22},
	Title = {Pulmonary Kinematics From Hyperpolarized Helium-3 Tagged Magnetic Resonance Imaging},
	Year = {2007}}

@inbook{Tustison2007b,
	Author = {Nicholas J. Tustison and Amir A. Amini},
	Chapter = {Analysis of 4-D Cardiac MR Data with NURBS Deformable Models: Temporal Fitting Strategy and Nonrigid Registration.},
	Editor = {Jasjit S. Suri and Aly Farag},
	Publisher = {Springer Publishers},
	Timestamp = {2007.09.25},
	Title = {Parametric and Geometric Deformable Models: An application in Biomaterials and Medical Imagery},
	Year = {2007}}

@article{Tustison2006c,
	Abstract = {We present research in which both left and right ventricular deformation is estimated from tagged cardiac magnetic resonance imaging using volumetric deformable models constructed from nonuniform rational B-splines (NURBS). The four model types considered and compared for the left ventricle include two Cartesian NURBS models--one with a cylindrical parameter assignment and one with a prolate spheroidal parameter assignment. The remaining two are non-Cartesian, i.e., prolate spheroidal and cylindrical each with their respective prolate spheroidal and cylindrical parameter assignment regimes. These choices were made based on the typical shape of the left ventricle. For each frame starting with end-diastole, a NURBS model is constructed by fitting two surfaces with the same parameterization to the corresponding set of epicardial and endocardial contours from which a volumetric model is created. Using normal displacements of the three sets of orthogonal tag planes as well as displacements of contour/tag line intersection points and tag plane intersection points, one can solve for the optimal homogeneous coordinates, in a weighted least squares sense, of the control points of the deformed NURBS model at end-diastole using quadratic programming. This allows for subsequent nonrigid registration of the biventricular model at end-diastole to all later time frames. After registration of the model to all later time points, the registered NURBS models are temporally lofted in order to create a comprehensive four-dimensional NURBS model. From the lofted model, we can extract three-dimensional myocardial deformation fields and corresponding Lagrangian and Eulerian strain maps which are local measures of nonrigid deformation. The results show that, in the case of simulated data, the quadratic Cartesian NURBS models with the cylindrical and prolate spheroidal parameter assignments outperform their counterparts in predicting normal strain. The decreased complexity associated with the Cartesian model with the cylindrical parameter assignment prompted its use for subsequent calculations. Lagrangian strains in three canine data, a normal human, and a patient with history of myocardial infarction are presented. Eulerian strains for the normal human data are also included.},
	Author = {Nicholas J Tustison and Amir A Amini},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {Algorithms, Animals, Artificial Intelligence, Cardiovascular, Computer Simulation, Computer-Assisted, Dogs, Elasticity, Extramural, Heart Ventricles, Humans, Image Enhancement, Image Interpretation, Imaging, Information Storage and Retrieval, Magnetic Resonance Imaging, Mechanical, Models, Myocardial Contraction, N.I.H., Reproducibility of Results, Research Support, Sensitivity and Specificity, Stress, Subtraction Technique, Three-Dimensional, Ventricular Function, 16398418},
	Month = {Jan},
	Number = {1},
	Pages = {94--112},
	Pmid = {16398418},
	Timestamp = {2006.04.12},
	Title = {{B}iventricular myocardial strains via nonrigid registration of anatomical {NURBS} model [corrected]},
	Volume = {25},
	Year = {2006}}

@inproceedings{Tustison2004a,
	Author = {N. J. Tustison and A. A. Amini},
	Booktitle = {Proceedings of SPIE: Medical Imaging},
	Month = {February},
	Timestamp = {2007.09.25},
	Title = {Myocardial Kinematics Based on Tagged MRI From Geometric Deformable Models},
	Year = {2004}}

@article{Tustison2009,
	Abstract = {Previous contributions to both the research and open source software communities detailed a generalization of a fast scalar field fitting technique for cubic B-splines based on the work originally proposed by Lee . One advantage of our proposed generalized B-spline fitting approach is its immediate application to a class of nonrigid registration techniques frequently employed in medical image analysis. Specifically, these registration techniques fall under the rubric of free-form deformation (FFD) approaches in which the object to be registered is embedded within a B-spline object. The deformation of the B-spline object describes the transformation of the image registration solution. Representative of this class of techniques, and often cited within the relevant community, is the formulation of Rueckert who employed cubic splines with normalized mutual information to study breast deformation. Similar techniques from various groups provided incremental novelty in the form of disparate explicit regularization terms, as well as the employment of various image metrics and tailored optimization methods. For several algorithms, the underlying gradient-based optimization retained the essential characteristics of Rueckert's original contribution. The contribution which we provide in this paper is two-fold: 1) the observation that the generic FFD framework is intrinsically susceptible to problematic energy topographies and 2) that the standard gradient used in FFD image registration can be modified to a well-understood preconditioned form which substantially improves performance. This is demonstrated with theoretical discussion and comparative evaluation experimentation.},
	Author = {Nicholas J Tustison and Brian B Avants and James C Gee},
	Doi = {10.1109/TIP.2008.2010072},
	Journal = {IEEE Trans Image Process},
	Month = {Mar},
	Number = {3},
	Pages = {624--635},
	Pmid = {19171516},
	Timestamp = {2009.03.03},
	Title = {Directly manipulated free-form deformation image registration.},
	Url = {http://dx.doi.org/10.1109/TIP.2008.2010072},
	Volume = {18},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TIP.2008.2010072}}

@inproceedings{Tustison2007c,
	Author = {Nicholas J. Tustison and Brian B. Avants and James C. Gee},
	Booktitle = {Proceedings of Mathematical Methods in Biomedical Image Analysis},
	Timestamp = {2007.12.11},
	Title = {Directly Manipulated {FFD} {B}-Spline Image Registration},
	Year = {2007}}

@inproceedings{Tustison2007g,
	Author = {Tustison, Nicholas J. and Avants, Brian B. and Gee, James C.},
	Booktitle = {Proc. IEEE 11th International Conference on Computer Vision ICCV 2007},
	Doi = {10.1109/ICCV.2007.4409161},
	Issn = {1550-5499},
	Pages = {1--8},
	Timestamp = {2008.02.10},
	Title = {Improved FFD B-Spline Image Registration},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/ICCV.2007.4409161}}

@inproceedings{Tustison2006a,
	Author = {Nicholas J. Tustison and Brian B. Avants and Tessa A. Sundaram and Jeffrey T. Duda and James C. Gee},
	Booktitle = {Workshop on Biomedical Image Registration},
	Timestamp = {2006.07.07},
	Title = {A Generalization of Free-Form Deformation Image Registration Within the ITK Finite Element Framework},
	Year = {2006}}

@conference{Tustison2008a,
	Author = {Nicholas J. Tustison and Suyash P. Awate and Jing Cai and Talissa A. Altes and G. Wilson Miller and Eduard E. de Lange and John P. Mugler III and James C. Gee},
	Booktitle = {Proc. of the International Symposium on Biomedical Imaging},
	Note = {submitted},
	Pages = {772},
	Timestamp = {2009.05.18},
	Title = {Point-Set Registration of Tagged {He-3} Images Using A Structurally-Based Jensen-Shannon Divergence Measure Within A Deterministic Annealing Framework},
	Year = {2008}}

@inproceedings{Tustison2009a,
	Author = {Nicholas J. Tustison and Suyash P. Awate and Gang Song and Tessa S. Cook and James C. Gee},
	Booktitle = {Proceedings of Information Processing in Medical Imaging},
	Timestamp = {2009.03.30},
	Title = {A New Information-Theoretic Measure to Control the Robustness-Sensitivity Trade-Off for DMFFD Point-Set Registration},
	Year = {2009}}

@conference{Tustison2008,
	Author = {Nicholas J. Tustison and Jing Cai and Talissa A. Altes and G. Wilson Miller and Eduard E. de Lange and John P. Mugler III and James C. Gee},
	Booktitle = {Proc. of the 16th Annual Meeting of ISMRM},
	Note = {submitted},
	Timestamp = {2009.05.18},
	Title = {Pulmonary Kinematics From {3-D} Hyperpolarized Helium-3 Tagged Magnetic Resonance Imaging},
	Year = {2008}}

@conference{Tustison2008e,
	Author = {Nicholas J. Tustison and Jing Cai and Talissa A. Altes and G. Wilson Miller and Eduard E. de Lange and John P. Mugler III and James C. Gee},
	Booktitle = {Proceedings of the International Society for Magnetic Resonance in Medicine},
	Note = {submitted},
	Timestamp = {2008.01.02},
	Title = {Pulmonary Kinematics From 3-D Hyperpolarized Helium-3 Tagged Magnetic Resonance Imaging},
	Year = {2008}}

@article{Tustison2003,
	Abstract = {Current research investigating the modeling of left ventricular dynamics for accurate clinical assessment of cardiac function is extensive. Magnetic resonance (MR) tagging is a functional imaging method which allows for encoding of a grid of signal voids on cardiac MR images, providing a mechanism for noninvasive measurement of intramural tissue deformations, in vivo. We present a novel technique of employing a four-dimensional (4-D) B-spline model which permits concurrent determination of myocardial beads and myocardial strains. The method entails fitting the knot planes of the 4-D B-spline model for fixed times to a sequence of triplets of orthogonal sets of tag surfaces for all imaged volumetric frames within the constraints of the model's spatio-temporal internal energy. From a three-dimensional (3-D) displacement field, the corresponding long and short-axis Lagrangian normal, shear, and principal strain maps are produced. As an important byproduct, the points defined by the 3-D intersections of the triplets of orthogonal tag planes, which we refer to as myocardial beads, can easily be determined by our model. Displaying the beads as a movie loop allows for the visualization of the nonrigid movement of the left ventricle in 3-D.},
	Journal = {IEEE Trans Biomed Eng},
	Keywords = {Algorithms, Automated, Heart Ventricles, Humans, Image Enhancement, Imaging, Left, Magnetic Resonance Imaging, Mechanical, Motion, Movement, P.H.S., Pattern Recognition, Research Support, Stress, Three-Dimensional, U.S. Gov't, Ventricular Function, 12892332},
	Month = {Aug},
	Number = {8},
	Pages = {1038--1040},
	Pmid = {12892332},
	Timestamp = {2006.04.12},
	Title = {{M}yocardial kinematics from tagged {MRI} based on a 4-{D} {B}-spline model.},
	Volume = {50},
	Year = {2003}}

@article{Tustison2009c,
	Author = {N. J. Tustison and J. C. Gee},
	Journal = {Insight Journal},
	Timestamp = {2009.05.18},
	Title = {N4ITK: Nick's N3 ITK Implementation for MRI Bias Field Correction},
	Year = {2009}}

@article{Tustison2007e,
	Author = {Nicholas J. Tustison and James. C. Gee},
	Journal = {Insight Journal},
	Timestamp = {2008.01.02},
	Title = {Image Kernel Convolution},
	Url = {http://hdl.handle.net/1926/1323},
	Year = {2007},
	Bdsk-Url-1 = {http://hdl.handle.net/1926/1323}}

@inproceedings{Tustison2006b,
	Author = {N. J. Tustison and J. C. Gee},
	Booktitle = {Proc. Third International Workshop Medical Imaging and Augmented Reality},
	Pages = {76-83},
	Timestamp = {2006.12.20},
	Title = {Generalized $n$-{D} ${C}^k$ {B}-spline scattered data approximation with confidence values},
	Year = {2006}}

@article{Tustison2005,
	Author = {N. J. Tustison and J. C. Gee},
	Journal = {Insight Journal},
	Pages = {published online},
	Timestamp = {2009.05.18},
	Title = {${N}$-{D} ${C}^k$ {B}-Spline Scattered Data Approximation},
	Url = {http://hdl.handle.net/1926/140},
	Year = {2005},
	Bdsk-Url-1 = {http://hdl.handle.net/1926/140}}

@article{Tustison2007,
	Author = {Nicholas J. Tustison and Marcelo Siqueira and James C. Gee},
	Journal = {Insight Journal},
	Pages = {published online},
	Timestamp = {2009.05.18},
	Title = {Well-Composedness and the Topological Repairing of {2-D} and {3-D} Digital Images},
	Url = {http://hdl.handle.net/1926/470},
	Year = {2007},
	Bdsk-Url-1 = {http://hdl.handle.net/1926/470}}

@article{Tustison2006,
	Author = {Nicholas J. Tustison and Marcelo Siqueira and James C. Gee},
	Journal = {Insight Journal},
	Month = {February},
	Pages = {published online},
	Timestamp = {2009.05.18},
	Title = {N-{D} Linear Time Exact Signed Euclidean Distance Transform},
	Url = {http://hdl.handle.net/1926/171},
	Year = {2006},
	Bdsk-Url-1 = {http://hdl.handle.net/1926/171}}

@article{Tustison2008b,
	Author = {N. J. Tustison and P. A. Yushkevich and J. C. Gee},
	Journal = {Insight Journal},
	Pages = {published online},
	Timestamp = {2009.05.18},
	Title = {Live-Wire-ing the Insight Toolkit with Intelligent Scissors},
	Year = {2008}}

@article{Tustison2008c,
	Author = {N. J. Tustison and H. Zhang and G. Lehmann and P. Yushkevich and J. C. Gee},
	Journal = {Insight Journal},
	Timestamp = {2008.10.19},
	Title = {Meeting Andy Warhol Somewhere Over the Rainbow: RGB Colormapping and ITK},
	Url = {http://hdl.handle.net/1926/1452},
	Year = {2008},
	Bdsk-Url-1 = {http://hdl.handle.net/1926/1452}}

@article{Unser1991,
	Author = {Michael Unser and Akram Aldroubi and Murray Eden},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {3},
	Owner = {tustison},
	Pages = {277-285},
	Title = {Fast B-Spline Transforms for Continuous Image Representation and Interpolation},
	Volume = {13},
	Year = {1991}}

@article{Uppaluri1999,
	Author = {R. Uppaluri and E. A. Hoffman and M. Sonka and P. G. Hartley and G. W. Hunninghake and G. McLennan},
	Journal = {Am J Respir Crit Care Med},
	Month = {Aug},
	Number = {2},
	Pages = {648--654},
	Timestamp = {2009.05.18},
	Title = {Computer recognition of regional lung disease patterns.},
	Volume = {160},
	Year = {1999}}

@article{Uppaluri1999a,
	Author = {R. Uppaluri and E. A. Hoffman and M. Sonka and G. W. Hunninghake and G. McLennan},
	Journal = {Am J Respir Crit Care Med},
	Month = {Feb},
	Number = {2},
	Pages = {519--525},
	Timestamp = {2009.05.18},
	Title = {Interstitial lung disease: A quantitative study using the adaptive multiple feature method.},
	Volume = {159},
	Year = {1999}}

@article{Uppaluri1997,
	Author = {R. Uppaluri and T. Mitsa and M. Sonka and E. A. Hoffman and G. McLennan},
	Journal = {Am J Respir Crit Care Med},
	Month = {Jul},
	Number = {1},
	Pages = {248--254},
	Timestamp = {2009.05.18},
	Title = {Quantification of pulmonary emphysema from lung computed tomography images.},
	Volume = {156},
	Year = {1997}}

@article{Vanzella2004,
	Author = {Vanzella, W. and Pellegrino, F.A. and Torre, V.},
	Doi = {10.1109/TPAMI.2004.15},
	Journal = IEEE_J_PAMI,
	Month = {June},
	Number = {6},
	Pages = {804--809},
	Timestamp = {2008.11.26},
	Title = {Self-adaptive regularization},
	Volume = {26},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2004.15}}

@article{Vercauteren2009,
	Abstract = {We propose an efficient non-parametric diffeomorphic image registration algorithm based on Thirion's demons algorithm. In the first part of this paper, we show that Thirion's demons algorithm can be seen as an optimization procedure on the entire space of displacement fields. We provide strong theoretical roots to the different variants of Thirion's demons algorithm. This analysis predicts a theoretical advantage for the symmetric forces variant of the demons algorithm. We show on controlled experiments that this advantage is confirmed in practice and yields a faster convergence. In the second part of this paper, we adapt the optimization procedure underlying the demons algorithm to a space of diffeomorphic transformations. In contrast to many diffeomorphic registration algorithms, our solution is computationally efficient since in practice it only replaces an addition of displacement fields by a few compositions. Our experiments show that in addition to being diffeomorphic, our algorithm provides results that are similar to the ones from the demons algorithm but with transformations that are much smoother and closer to the gold standard, available in controlled experiments, in terms of Jacobians.},
	Author = {Tom Vercauteren and Xavier Pennec and Aymeric Perchant and Nicholas Ayache},
	Doi = {10.1016/j.neuroimage.2008.10.040},
	Institution = {Mauna Kea Technologies, 9 rue d'Enghien, 75010 Paris, France. tom.vercauteren@maunakeatech.com},
	Journal = {Neuroimage},
	Keywords = {Algorithms; Humans; Image Processing, Computer-Assisted},
	Month = {Mar},
	Number = {1 Suppl},
	Pages = {S61--S72},
	Pii = {S1053-8119(08)01168-3},
	Pmid = {19041946},
	Timestamp = {2009.06.06},
	Title = {Diffeomorphic demons: efficient non-parametric image registration.},
	Url = {http://dx.doi.org/10.1016/j.neuroimage.2008.10.040},
	Volume = {45},
	Year = {2009},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuroimage.2008.10.040}}

@article{Vercauteren2007,
	Author = {Tom Vercauteren and Xavier Pennec and Aymeric Perchant and Nicholas Ayache},
	Journal = {Insight Journal---2007 MICCAI Open Science Workshop},
	Timestamp = {2009.06.06},
	Title = {Diffeomorphic Demons Using ITK's Finite Difference Solver Hierarchy},
	Year = {2007}}

@article{Vignola2004,
	Abstract = {It is not known whether sputum elastase, metalloproteinase (MMP)-9 and tissue-inhibitor metalloproteinase (TIMP)-1 are related to structural changes of the airways, as assessed by high-resolution computed tomography (HRCT) scan. The relationships between these markers and the magnitude of structural changes of the airways in asthma and chronic obstructive pulmonary disease (COPD) were assessed. Induced sputum and HRCT scan were performed in 30 asthmatics (14 mild and 16 severe) and in 12 patients with COPD. A greater extent of HRCT scan abnormalities was found in COPD than in severe and mild asthmatics. HRCT scan abnormalities correlated with the degree of airway obstruction in COPD and in severe asthma. HRCT scan abnormalities also correlated with the levels of sputum elastase both in COPD and in severe asthma. HRCT scan abnormalities were associated with sputum MMP-9/TIMP-1 ratio in mild asthma, severe asthma and COPD. In conclusion, this study demonstrates that sputum elastase and the metalloproteinase-9/tissue-inhibitor metalloproteinase-1 ratio are associated with the magnitude of high-resolution computed tomography scan abnormalities of the airways in asthma and chronic obstructive pulmonary disease, and suggests that the levels of these markers reflect the extent of structural changes of the airways.},
	Author = {A. M. Vignola and F. Paganin and L. Capieu and N. Scichilone and M. Bellia and L. Maakel and V. Bellia and P. Godard and J. Bousquet and P. Chanez},
	Doi = {10.1183/09031936.04.00032603},
	Journal = {Eur Respir J},
	Keywords = {Adult; Aged; Asthma; Female; Humans; Male; Matrix Metalloproteinase 9; Middle Aged; Pancreatic Elastase; Pulmonary Disease, Chronic Obstruct; Respiratory Function Tests; Sputum; Statistics, Nonparametric; Tissue Inhibitor of Metalloproteinase-1; Tomography, X-Ray Computed; ive},
	Month = {Dec},
	Number = {6},
	Pages = {910--917},
	Pii = {24/6/910},
	Pmid = {15572531},
	Timestamp = {2007.09.09},
	Title = {Airway remodelling assessed by sputum and high-resolution computed tomography in asthma and COPD.},
	Url = {http://dx.doi.org/10.1183/09031936.04.00032603},
	Volume = {24},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1183/09031936.04.00032603}}

@article{Vikgren2003,
	Journal = {Acta Radiol},
	Month = {Sep},
	Number = {5},
	Pages = {517--524},
	Timestamp = {2009.05.18},
	Title = {Value of air trapping in detection of small airways disease in smokers.},
	Volume = {44},
	Year = {2003}}

@inproceedings{Vincent2003,
	Author = {Pascal Vincent and Yoshua Bengio},
	Booktitle = {Advances in Neural Information Prcessing Systems},
	Chapter = {Manifold parzen Windows},
	Editor = {S. Thrun and S. Becker and K. Obermayer},
	Pages = {825-832},
	Publisher = {MIT Press},
	Timestamp = {2007.12.11},
	Title = {Manifold parzen windows},
	Year = {2003}}

@article{Vinciarelli2005,
	Author = {Vinciarelli, A.},
	Doi = {10.1109/TPAMI.2005.248},
	Journal = IEEE_J_PAMI,
	Month = {Dec.},
	Number = {12},
	Pages = {1882--1895},
	Timestamp = {2008.11.26},
	Title = {Noisy text categorization},
	Volume = {27},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2005.248}}

@article{Viola1997,
	Author = {Paula Viola and William M. Wells},
	Journal = {International Journal of Computer Vision},
	Number = {2},
	Owner = {tustison},
	Pages = {137-154},
	Title = {Alignment by Maximization of Mutual Information},
	Volume = {24},
	Year = {1997}}

@article{Voorhees2005,
	Abstract = {In this work MRI-based spirometry is presented as a method for noninvasively assessing pulmonary mechanical function on a regional basis. A SPAMM tagging sequence was modified to allow continuous dynamic imaging of the lungs during respiration. A motion-tracking algorithm was developed to track material regions from time-resolved grid-tagged images. Experiments were performed to image the lungs during quiet breathing and volumetric strain was calculated from the measured displacement maps. Regional volume calculations, derived from volumetric strain, were integrated over the entire lung and compared to segmented volume calculations with good agreement. Results from this work demonstrate that MRI spirometry has the potential to become a clinically useful tool for measuring regional ventilation and assessing pulmonary diseases that regionally affect the mechanical function of the lung.},
	Author = {Abram Voorhees and Jing An and Kenneth I Berger and Roberta M Goldring and Qun Chen},
	Doi = {10.1002/mrm.20682},
	Journal = {Magn Reson Med},
	Keywords = {Adult; Algorithms; Artificial Intelligence; Female; Humans; Image Enhancement; Image Interpretation, Computer-Assisted; Imaging, Three-Dimensional; Lung; Magnetic Resonance Imaging; Male; Middle Aged; Pattern Recognition, Automated; Pulmonary Ventilation; Reproducibility of Results; Research Support, N.I.H., Extramural; Respiratory Mechanics; Sensitivity and Specificity; Spirometry; Tidal Volume},
	Month = {Nov},
	Number = {5},
	Pages = {1146--1154},
	Pmid = {16217776},
	Timestamp = {2006.12.20},
	Title = {Magnetic resonance imaging-based spirometry for regional assessment of pulmonary function.},
	Url = {http://dx.doi.org/10.1002/mrm.20682},
	Volume = {54},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/mrm.20682}}

@article{Wang2008a,
	Author = {Wang, F. and Vemuri, B.C. and Rangarajan, A. and Eisenschenk, S.J.},
	Doi = {10.1109/TPAMI.2007.70829},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Month = {Nov.},
	Number = {11},
	Pages = {2011--2022},
	Timestamp = {2008.11.26},
	Title = {Simultaneous Nonrigid Registration of Multiple Point Sets and Atlas Construction},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70829}}

@inproceedings{Wang2006,
	Author = {Fei Wang and Baba C. Vemuri and Anand Rangarajan and Ilona M. Schmalfuss and Stephan J. Eisenschenk},
	Booktitle = {Proceedings of the European Conference on Computer Vision},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Pages = {551-563},
	Timestamp = {2007.12.11},
	Title = {Simultaneous Nonrigid Registration of Multiple Point-Sets and Atlas Construction},
	Volume = {3},
	Year = {2006}}

@article{Wang2008,
	Author = {Wang, J.Z. and Geman, D. and Jiebo Luo and Gray, R.M.},
	Doi = {10.1109/TPAMI.2008.231},
	Journal = IEEE_J_PAMI,
	Month = {Nov.},
	Number = {11},
	Pages = {1873--1876},
	Timestamp = {2008.11.26},
	Title = {Real-World Image Annotation and Retrieval: An Introduction to the Special Section},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2008.231}}

@article{Wang2003,
	Author = {Yongmei Wang and Bradley S. Peterson and Lawrence H. Staib},
	Journal = {Computer Vision and Image Understanding},
	Pages = {252-271},
	Timestamp = {2006.07.07},
	Title = {3D Brain surface matching based on geodesics and local geometry},
	Volume = {89},
	Year = {2003}}

@article{Wang2000,
	Author = {Yongmei Wang and Lawrence H. Staib},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {7},
	Owner = {tustison},
	Pages = {738-743},
	Title = {Boundary Finding with Prior Shape and Smoothness Models},
	Volume = {22},
	Year = {2000}}

@article{Wang2004,
	Author = {Yizhou Wang and Song-Chun Zhu},
	Doi = {10.1109/TPAMI.2004.76},
	Journal = IEEE_J_PAMI,
	Month = {Oct.},
	Number = {10},
	Pages = {1348--1363},
	Timestamp = {2008.11.26},
	Title = {Analysis and synthesis of textured motion: particles and waves},
	Volume = {26},
	Year = {2004},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2004.76}}

@article{Warfield2004,
	Author = {Simon K Warfield and Kelly H Zou and William M Wells},
	Journal = {IEEE Trans Med Imaging},
	Month = {Jul},
	Number = {7},
	Pages = {903--921},
	Timestamp = {2009.05.18},
	Title = {Simultaneous truth and performance level estimation (STAPLE): an algorithm for the validation of image segmentation.},
	Volume = {23},
	Year = {2004}}

@article{Wassermann2002,
	Author = {Klaus Wassermann},
	Journal = {Chest},
	Keywords = {Asthma; Chronic Disease; Humans; Lung Diseases, Interstitial; Respiratory Mechanics},
	Month = {Mar},
	Number = {3},
	Pages = {673--674},
	Pmid = {11888939},
	Timestamp = {2007.09.08},
	Title = {Is asthma another interstitial lung disease?},
	Volume = {121},
	Year = {2002}}

@article{Wells1996,
	Author = {William M. Wells and Paul Viola and Hideki Atsumi and Shin Nakajima and Ron Kikinis},
	Journal = {Medical Image Analysis},
	Number = {1},
	Owner = {tustison},
	Pages = {33-51},
	Title = {Multi-modal volume registration by maximization of mutual information},
	Volume = {1},
	Year = {1996}}

@article{Weruaga2004,
	Author = {Luis Weruaga and Rafael Verdu and Juan Morales},
	Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
	Number = {12},
	Owner = {tustison},
	Pages = {1568-1578},
	Title = {Frequency Domain Formulation of Active Parametric Deformable Models},
	Volume = {26},
	Year = {2004}}

@article{Westin2002,
	Abstract = {This paper presents processing and visualization techniques for Diffusion Tensor Magnetic Resonance Imaging (DT-MRI). In DT-MRI, each voxel is assigned a tensor that describes local water diffusion. The geometric nature of diffusion tensors enables us to quantitatively characterize the local structure in tissues such as bone, muscle, and white matter of the brain. This makes DT-MRI an interesting modality for image analysis. In this paper we present a novel analytical solution to the Stejskal-Tanner diffusion equation system whereby a dual tensor basis, derived from the diffusion sensitizing gradient configuration, eliminates the need to solve this equation for each voxel. We further describe decomposition of the diffusion tensor based on its symmetrical properties, which in turn describe the geometry of the diffusion ellipsoid. A simple anisotropy measure follows naturally from this analysis. We describe how the geometry or shape of the tensor can be visualized using a coloring scheme based on the derived shape measures. In addition, we demonstrate that human brain tensor data when filtered can effectively describe macrostructural diffusion, which is important in the assessment of fiber-tract organization. We also describe how white matter pathways can be monitored with the methods introduced in this paper. DT-MRI tractography is useful for demonstrating neural connectivity (in vivo) in healthy and diseased brain tissue.},
	Author = {C-F Westin and SE Maier and H Mamata and A Nabavi and FA Jolesz and R Kikinis},
	Journal = {Med Image Anal},
	Keywords = {Brain, Data Display, Humans, Image Processing, Computer-Assisted, Magnetic Resonance Imaging, Models, Theoretical, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, P.H.S., Sensitivity and Specificity, 12044998},
	Month = {Jun},
	Number = {2},
	Owner = {tustison},
	Pages = {93-108},
	Pii = {S1361841502000531},
	Title = {Processing and visualization for diffusion tensor {MRI}.},
	Volume = {6},
	Year = {2002}}

@article{Wilkinson2008,
	Author = {Wilkinson, M.H.F. and Hui Gao and Hesselink, W.H. and Jonker, J.-E. and Meijster, A.},
	Doi = {10.1109/TPAMI.2007.70836},
	Journal = IEEE_J_PAMI,
	Month = {Oct.},
	Number = {10},
	Pages = {1800--1813},
	Timestamp = {2008.11.26},
	Title = {Concurrent Computation of Attribute Filters on Shared Memory Parallel Machines},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70836}}

@inproceedings{Wolf2004,
	Author = {Ivo Wolf and Marcus Vetter and Ingmar Wegner and Marco Nolden and Thomas Bottger and Mark Hastenteufel and Max Shobinger and Tobias Kunert and Hans-Peter Meinzer},
	Booktitle = {Proceedings of the SPIE: Medical Imaging: Visualization, Image-Guided Procedures, and Display},
	Owner = {tustison},
	Title = {The Medical Imaging Interaction Toolkit (MITK) -- a toolkit facilitating the creation of interactive software by extending VTK and ITK},
	Year = {2004}}

@article{Wolpert1997,
	Author = {Wolpert, D.H. and Macready, W.G.},
	Doi = {10.1109/4235.585893},
	Journal = {IEEE Transactions on Evolutionary Computation},
	Month = {April},
	Number = {1},
	Pages = {67--82},
	Timestamp = {2009.03.03},
	Title = {No free lunch theorems for optimization},
	Volume = {1},
	Year = {1997},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/4235.585893}}

@article{wolpert1997no,
	Author = {Wolpert, David H and Macready, William G},
	Journal = {Evolutionary Computation, IEEE Transactions on},
	Number = {1},
	Owner = {stnava},
	Pages = {67--82},
	Publisher = {IEEE},
	Timestamp = {2014.04.29},
	Title = {No free lunch theorems for optimization},
	Volume = {1},
	Year = {1997}}

@article{Wong2008,
	Author = {Wong, Kwan-Yee K. and Zhang, Guoqiang and Liang, Chen and Zhang, Hui},
	Doi = {10.1109/TPAMI.2008.169},
	Journal = IEEE_J_PAMI,
	Month = {Dec.},
	Number = {12},
	Pages = {2243--2248},
	Timestamp = {2008.11.26},
	Title = {1D Camera Geometry and Its Application to the Self-Calibration of Circular Motion Sequences},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2008.169}}

@article{Wood1995,
	Author = {S. A. Wood and E. A. Zerhouni and J. D. Hoford and E. A. Hoffman and W. Mitzner},
	Journal = {J Appl Physiol},
	Month = {Nov},
	Number = {5},
	Pages = {1687--1697},
	Timestamp = {2009.05.18},
	Title = {Measurement of three-dimensional lung tree structures by using computed tomography.},
	Volume = {79},
	Year = {1995}}

@article{Woodhouse2005,
	Abstract = {PURPOSE: To use a combination of helium-3 (3-He) magnetic resonance imaging (MRI) and proton single-shot fast spin echo (SSFSE) to compare ventilated lung volumes in groups of "healthy" smokers, smokers diagnosed with moderate chronic obstructive pulmonary disease (COPD), and never-smokers. MATERIALS AND METHODS: All study participants were assessed with spirometry prior to imaging. 3-He images were collected during an arrested breath hold, after inhaling a mixture of 200 mL of hyperpolarized 3-He/800 mL of N2. Proton SSFSE images were acquired after inhaling 1 liter of room air. The ventilated volume for each study participant was calculated from the 3-He images, and a ratio was calculated to give a percentage ventilated lung volume. RESULTS: Never-smokers exhibited a 90\% mean ventilated volume. The mean ventilated lung volumes for healthy smokers and smokers diagnosed with COPD were 75.2\% and 67.6\%, respectively. No correlation with spirometry was demonstrated for either of the smoking groups. CONCLUSION: Combined 3-He/Proton SSFSE MRI of the lungs is a noninvasive method, using nonionizing radiation, which demonstrates ventilated airspaces and enables the calculation of ventilated lung volumes. This method appears to be sensitive to early obstructive changes in the lungs of smokers.},
	Author = {Neil Woodhouse and Jim M Wild and Martyn N J Paley and Stanislao Fichele and Zead Said and Andrew J Swift and Edwin J R van Beek},
	Doi = {10.1002/jmri.20290},
	Journal = {J Magn Reson Imaging},
	Keywords = {Adult; Female; Helium; Humans; Isotopes; Lung Volume Measurements; Magnetic Resonance Imaging; Male; Middle Aged; Pulmonary Disease, Chronic Obstructive; Respiratory Physiology; Smoking},
	Month = {Apr},
	Number = {4},
	Pages = {365--369},
	Pmid = {15779032},
	Timestamp = {2007.06.06},
	Title = {Combined helium-3/proton magnetic resonance imaging measurement of ventilated lung volumes in smokers compared to never-smokers.},
	Url = {http://dx.doi.org/10.1002/jmri.20290},
	Volume = {21},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1002/jmri.20290}}

@article{Wu2003,
	Abstract = {Complete knowledge of myocardial structure, metabolism, and function is crucial to understanding the response of the heart to injury such as ischemia. Increasingly, this type of knowledge is required at multiple levels, from that of the isolated myocyte to the functioning organism, to provide basic scientists and clinical investigators a common framework for translation of findings and information feedback. This article focuses on the utilization of imaging methods to assess myocardial viability in vivo. It discusses the advantages and pitfalls of different imaging techniques, with particular emphasis on available data in humans and large animal models. Because of their novelty and potential for accurate phenotyping of human pathophysiology, magnetic resonance modalities will be highlighted.},
	Doi = {10.1161/01.RES.0000103863.40055.E8},
	Journal = {Circ Res},
	Keywords = {Animals; Diagnostic Imaging; Echocardiography; Forecasting; Humans; Magnetic Resonance Imaging; Myocardial Infarction; Tomography, Emission-Computed; Tomography, Emission-Computed, Single-Photon},
	Month = {Dec},
	Number = {12},
	Pages = {1146--1158},
	Pii = {93/12/1146},
	Pmid = {14670830},
	Timestamp = {2007.09.09},
	Title = {Noninvasive imaging of myocardial viability: current techniques and future developments.},
	Url = {http://dx.doi.org/10.1161/01.RES.0000103863.40055.E8},
	Volume = {93},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1161/01.RES.0000103863.40055.E8}}

@article{Xavier2005,
	Author = {Xavier Pennec, Pierre Fillard, Nicholas Ayache},
	Journal = {International Journal of Computer Vision},
	Owner = {tustison},
	Title = {A Riemannian Framework for Tensor Computing},
	Year = {2005}}

@article{Xie2001,
	Author = {Hui Xie and Hong Qin},
	Journal = {International Journal of Shape Modeling},
	Number = {2},
	Owner = {tustison},
	Pages = {199-227},
	Title = {A Novel Optimization Approach to the Effective Computation of NURBS Knots},
	Volume = {7},
	Year = {2001}}

@article{Xie2004,
	Abstract = {Hierarchical B-splines have been widely used for shape modeling since their discovery by Forsey and Bartels. In this paper, we present an application of this concept, in the form of free-form deformation, to image registration by matching two images at increasing levels of detail. Results using MRI brain data are presented that demonstrate high degrees of matching while unnecessary distortions are avoided. We compare our results with the nonlinear ICP (Iterative Closest Point) algorithm (used for landmark-based registration) and optical flow (used for intensity-based registration).},
	Author = {Zhiyong Xie and Gerald E Farin},
	Journal = {IEEE Trans Vis Comput Graph},
	Keywords = {Algorithms, Brain, Comparative Study, Computer Graphics, Computer Simulation, Humans, Image Enhancement, Image Interpretation, Computer-Assisted, Imaging, Three-Dimensional, Information Storage and Retrieval, Magnetic Resonance Imaging, Numerical Analysis, Computer-Assisted, Pattern Recognition, Automated, Reproducibility of Results, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S., Research Support, U.S. Gov't, P.H.S., Sensitivity and Specificity, Signal Processing, Computer-Assisted, Subtraction Technique, User-Computer Interface, 15382700},
	Number = {1},
	Owner = {tustison},
	Pages = {85-94},
	Title = {Image registration using hierarchical {B}-splines.},
	Volume = {10},
	Year = {2004}}

@article{Xu2006,
	Author = {Ye Xu and Edwin J R van Beek and Yu Hwanjo and Junfeng Guo and Geoffrey McLennan and Eric A Hoffman},
	Journal = {Acad Radiol},
	Month = {Aug},
	Number = {8},
	Pages = {969--978},
	Timestamp = {2009.05.18},
	Title = {Computer-aided classification of interstitial lung diseases via {MDCT}: {3D} adaptive multiple feature method (3D AMFM).},
	Volume = {13},
	Year = {2006}}

@article{Xu2008,
	Author = {Yilei Xu and Roy-Chowdhury, A.K.},
	Doi = {10.1109/TPAMI.2008.81},
	Journal = IEEE_J_PAMI,
	Month = {July},
	Number = {7},
	Pages = {1300--1307},
	Timestamp = {2008.11.26},
	Title = {Inverse Compositional Estimation of 3D Pose And Lighting in Dynamic Scenes},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2008.81}}

@article{Xu2006a,
	Author = {Ye Xu and Milan Sonka and Geoffrey McLennan and Junfeng Guo and Eric A Hoffman},
	Journal = {IEEE Trans Med Imaging},
	Month = {Apr},
	Number = {4},
	Pages = {464--475},
	Timestamp = {2009.05.18},
	Title = {{MDCT}-based {3-D} texture classification of emphysema and early smoking related lung pathologies.},
	Volume = {25},
	Year = {2006}}

@article{Xue2004,
	Author = {Zhong Xue and Dinggang Shen and Christos Davatzikos},
	Journal = {IEEE Transactions on Medical Imaging},
	Number = {10},
	Owner = {tustison},
	Pages = {1276-1290},
	Title = {Determining Correspondence in 3-D MR Brain Images Using Attribute Vectors as Morphological Signatures of Voxels},
	Volume = {23},
	Year = {2004}}

@article{Yan2008,
	Author = {Fei Yan and Christmas, W. and Kittler, J.},
	Doi = {10.1109/TPAMI.2007.70834},
	Journal = IEEE_J_PAMI,
	Month = {Oct.},
	Number = {10},
	Pages = {1814--1830},
	Timestamp = {2008.11.26},
	Title = {Layered Data Association Using Graph-Theoretic Formulation with Application to Tennis Ball Tracking in Monocular Sequences},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70834}}

@inproceedings{Yan1995,
	Author = {Michelle X. H. Yan and Joel S. Karp},
	Booktitle = {Proc. of Information Processing in Medical Imaging},
	Owner = {tustison},
	Title = {An Adaptive Bayesian Approach to Three-Dimensional MR Brain Segmentation},
	Year = {1995}}

@article{Yang2004,
	Author = {Jing Yang and Lawrence H. Staib and James S. Duncan},
	Journal = {IEEE Transactions on Medical Imaging},
	Number = {8},
	Owner = {tustison},
	Pages = {940-948},
	Title = {Neighbor-Constrained Segmentation With Level Set Based 3-D Deformable Models},
	Volume = {23},
	Year = {2004}}

@article{Yoo2005,
	Author = {Terry S Yoo and Dimitris N Metaxas},
	Doi = {10.1016/j.media.2005.04.008},
	Journal = {Med Image Anal},
	Keywords = {Databases, Factual; Diagnostic Imaging; Image Interpretation, Computer-Assisted; Information Dissemination; Medical Informatics Applications; National Library of Medicine (U.S.); Science; Software; United States},
	Month = {Dec},
	Number = {6},
	Pages = {503--506},
	Pii = {S1361-8415(05)00027-7},
	Pmid = {16169766},
	Timestamp = {2009.03.03},
	Title = {Open science--combining open data and open source software: medical image analysis with the Insight Toolkit.},
	Url = {http://dx.doi.org/10.1016/j.media.2005.04.008},
	Volume = {9},
	Year = {2005},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.media.2005.04.008}}

@article{Yu2008,
	Author = {Yu, Qiyao and Clausi, David A.},
	Doi = {10.1109/TPAMI.2008.15},
	Journal = IEEE_J_PAMI,
	Month = {Dec.},
	Number = {12},
	Pages = {2126--2139},
	Timestamp = {2008.11.26},
	Title = {IRGS: Image Segmentation Using Edge Penalties and Region Growing},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2008.15}}

@article{Yu1995,
	Author = {Tzu Yi Yu and Bharat K Soni},
	Journal = {Computer-Aided Design},
	Number = {2},
	Owner = {tustison},
	Pages = {147-157},
	Title = {Application of NURBS in numerical grid generation},
	Volume = {27},
	Year = {1995}}

@article{Yuan2007,
	Journal = {Chest},
	Month = {Aug},
	Number = {2},
	Pages = {617--623},
	Timestamp = {2009.05.18},
	Title = {The effects of radiation dose and {CT} manufacturer on measurements of lung densitometry.},
	Volume = {132},
	Year = {2007}}

@article{Yushkevich2006,
	Abstract = {Active contour segmentation and its robust implementation using level set methods are well-established theoretical approaches that have been studied thoroughly in the image analysis literature. Despite the existence of these powerful segmentation methods, the needs of clinical research continue to be fulfilled, to a large extent, using slice-by-slice manual tracing. To bridge the gap between methodological advances and clinical routine, we developed an open source application called ITK-SNAP, which is intended to make level set segmentation easily accessible to a wide range of users, including those with little or no mathematical expertise. This paper describes the methods and software engineering philosophy behind this new tool and provides the results of validation experiments performed in the context of an ongoing child autism neuroimaging study. The validation establishes SNAP intrarater and interrater reliability and overlap error statistics for the caudate nucleus and finds that SNAP is a highly reliable and efficient alternative to manual tracing. Analogous results for lateral ventricle segmentation are provided.},
	Author = {Paul A Yushkevich and Joseph Piven and Heather Cody Hazlett and Rachel Gimpel Smith and Sean Ho and James C Gee and Guido Gerig},
	Doi = {10.1016/j.neuroimage.2006.01.015},
	Institution = {Penn Image Computing and Science Laboratory, Department of Radiology, University of Pennsylvania, PA 19104-6274, USA. pauly2@grasp.upenn.edu},
	Journal = {Neuroimage},
	Keywords = {Brain; Caudate Nucleus; Dominance, Cerebral; Humans; Image Processing, Computer-Assisted; Imaging, Three-Dimensional; Magnetic Resonance Imaging; Mathematical Computing; Software; Software Validation; User-Compu; ter Interface},
	Month = {Jul},
	Number = {3},
	Pages = {1116--1128},
	Pii = {S1053-8119(06)00063-2},
	Pmid = {16545965},
	Timestamp = {2008.05.21},
	Title = {User-guided 3D active contour segmentation of anatomical structures: significantly improved efficiency and reliability.},
	Url = {http://dx.doi.org/10.1016/j.neuroimage.2006.01.015},
	Volume = {31},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.neuroimage.2006.01.015}}

@article{Zanibbi2002,
	Author = {Zanibbi, R. and Blostein, D. and Cordy, J.R.},
	Doi = {10.1109/TPAMI.2002.1046157},
	Journal = IEEE_J_PAMI,
	Month = {Nov},
	Number = {11},
	Pages = {1455--1467},
	Timestamp = {2008.11.26},
	Title = {Recognizing mathematical expressions using tree transformation},
	Volume = {24},
	Year = {2002},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2002.1046157}}

@article{Zaporozhan2005,
	Author = {Julia Zaporozhan and Sebastian Ley and Ralf Eberhardt and Oliver Weinheimer and Svitlana Iliyushenko and Felix Herth and Hans-Ulrich Kauczor},
	Journal = {Chest},
	Month = {Nov},
	Number = {5},
	Pages = {3212--3220},
	Timestamp = {2009.05.18},
	Title = {Paired inspiratory/expiratory volumetric thin-slice {CT} scan for emphysema analysis: comparison of different quantitative evaluations and pulmonary function test.},
	Volume = {128},
	Year = {2005}}

@article{Zaporozhan2004,
	Abstract = {OBJECTIVE: To develop and evaluate a postprocessing tool to quantify ventilated split-lung volumes on the basis of (3)He-MRI and to apply it in patients after single-lung transplantation (SLTX). High-resolution CT (HRCT) was employed as a reference modality providing split air-filled lung volumes. Lung volumes derived from pulmonary function test results served as clinical parameters and were used as the "gold standard." MATERIAL AND METHODS: Eight patients (mean age, 54 years) with emphysema and six patients (mean age, 58 years) with idiopathic pulmonary fibrosis. All patients were evaluated following SLTX. HRCT was performed during inspiration (slice thickness, 1 mm; increment, 10 mm). For correlation with (3)He-MRI, HRCT images were reconstructed in coronal orientation to match the same anatomic levels. Aerated lung was determined by threshold-based segmentation of CT. (3)He-MRI was performed on a 1.5-T scanner using a two-dimensional, fast low-angle shot sequence in coronal orientation covering the whole lung after inhalation of a 300-mL bolus of hyperpolarized (3)He gas followed by normal room air for the rest of the tidal volume. Lung segmentation on (3)He-MRI was done using different thresholds. RESULTS: In emphysematous patients, (3)He-MRI showed excellent correlation (r = 0.9) with vital capacity, while CT correlated (r = 0.8) with total lung capacity. (3)He-MRI correlated well with CT (r > 0.8) for grafts and native fibrotic lungs. In emphysematous lungs, MRI showed a good correlation (r = 0.7) with the nonemphysematous lung volume from CT. Increasing thresholds in (3)He-MRI reveal differences between aerated and ventilated lung areas with a different distribution in emphysema and fibrosis. CONCLUSIONS: (3)He-MRI is superior to CT in emphysema to demonstrate ventilated lung areas that participate in gas exchange. In fibrosis, (3)He-MRI and CT have a similar impact. The decrease pattern and the intraindividual ratio between ventilation of native and transplanted lungs will have to be investigated as a new surrogate for the ventilatory follow-up in patients undergoing SLTX.},
	Journal = {Chest},
	Keywords = {-Assisted; Female; Helium; Humans; Image Processing, Computer; Isotopes; Lung; Lung Transplantation; Magnetic Resonance Imaging; Male; Middle A; Pulmonary Emphysema; Pulmonary Fibrosis; Pulmonary Gas Exchange; Respiratory Function Tests; Tomography, X-Ray Computed; Total Lung Capacity; Vital Capacity; ged},
	Month = {Jan},
	Number = {1},
	Pages = {173--181},
	Pmid = {14718438},
	Timestamp = {2007.06.06},
	Title = {Functional analysis in single-lung transplant recipients: a comparative study of high-resolution CT, 3He-MRI, and pulmonary function tests.},
	Volume = {125},
	Year = {2004}}

@article{Zaporozhan2006,
	Author = {Julia Zaporozhan and Sebastian Ley and Oliver Weinheimer and Ralf Eberhardt and Ioannis Tsakiris and Yasuhiro Noshi and Felix Herth and Hans-Ulrich Kauczor},
	Journal = {J Comput Assist Tomogr},
	Number = {3},
	Pages = {460--468},
	Timestamp = {2009.05.18},
	Title = {Multi-detector {CT} of the chest: influence of dose onto quantitative evaluation of severe emphysema: a simulation study.},
	Volume = {30},
	Year = {2006}}

@article{Zavaletta2007,
	Author = {Vanessa A Zavaletta and Brian J Bartholmai and Richard A Robb},
	Journal = {Acad Radiol},
	Month = {Jul},
	Number = {7},
	Pages = {772--787},
	Timestamp = {2009.05.18},
	Title = {High resolution multidetector {CT}-aided tissue analysis and quantification of lung fibrosis.},
	Volume = {14},
	Year = {2007}}

@article{Zerhouni1988,
	Author = {E. Zerhouni and D. Parish and W. Rogers and A. Yang and E. Shapiro},
	Journal = {Radiology},
	Pages = {59-63},
	Timestamp = {2006.12.20},
	Title = {Human heart: Tagging with {MR} Imaging---a method for noninvasive assessment of myocardial motion},
	Volume = {169},
	Year = {1988}}

@article{Zhang2004,
	Author = {Dengsheng Zhang and Guojun Lu},
	Journal = {Pattern Recognition},
	Owner = {tustison},
	Pages = {1-19},
	Title = {Review of shape representation and description techniques},
	Volume = {37},
	Year = {2004}}

@article{Zhang2007,
	Abstract = {Spatial normalization of diffusion tensor images plays a key role in voxel-based analysis of white matter (WM) group differences. Currently, it has been achieved using low-dimensional registration methods in the large majority of clinical studies. This paper aims to motivate the use of high-dimensional normalization approaches by generating evidence of their impact on the findings of such studies. Using an ongoing amyotrophic lateral sclerosis (ALS) study, we evaluated three normalization methods representing the current range of available approaches: low-dimensional normalization using the fractional anisotropy (FA), high-dimensional normalization using the FA, and high-dimensional normalization using full tensor information. Each method was assessed in terms of its ability to detect significant differences between ALS patients and controls. Our findings suggest that inadequate normalization with low-dimensional approaches can result in insufficient removal of shape differences which in turn can confound FA differences in a complex manner, and that utilizing high-dimensional normalization can both significantly minimize the confounding effect of shape differences to FA differences and provide a more complete description of WM differences in terms of both size and tissue architecture differences. We also found that high-dimensional approaches, by leveraging full tensor features instead of tensor-derived indices, can further improve the alignment of WM tracts.},
	Author = {Hui Zhang and Brian B Avants and Paul A Yushkevich and John H Woo and Sumei Wang and Leo F McCluskey and Lauren B Elman and Elias R Melhem and James C Gee},
	Institution = {Penn Image Computing and Science Laboratory, University of Pennsylvania, Philadelphia, PA 19104, USA.},
	Journal = {IEEE Trans Med Imaging},
	Keywords = {, Computer-Assisted; Adult; Aged; Algorithms; Amyotrophic Lateral Sclerosis; Artificial Intelligence; Brain; Diffusion Magnetic Resonance Imaging; Female; Humans; Image Enhancement; Image Interpretation; Imaging, Three-Dimensional; Male; Middle Aged; Nerve Fibers, Myelinated; Pattern Recognition, Automated; Reproducibility of Results; Sensitivity and Specificity},
	Month = {Nov},
	Number = {11},
	Pages = {1585--1597},
	Pmid = {18041273},
	Timestamp = {2008.06.03},
	Title = {High-dimensional spatial normalization of diffusion tensor images improves the detection of white matter differences: an example study using amyotrophic lateral sclerosis.},
	Volume = {26},
	Year = {2007}}

@article{Zhang,
	Author = {Hui Zhang and Paul Yushkevich and Daniel C. Alexander and James C. Gee},
	Owner = {tustison},
	Title = {Deformable Registration of Diffusion Tensor MR Images with Explicit Orientation Optimization}}

@article{Zhang2006,
	Author = {Li Zhang and Eric A Hoffman and Joseph M Reinhardt},
	Journal = {IEEE Trans Med Imaging},
	Month = {Jan},
	Number = {1},
	Pages = {1--16},
	Timestamp = {2009.05.18},
	Title = {Atlas-driven lung lobe segmentation in volumetric {X}-ray {CT} images.},
	Volume = {25},
	Year = {2006}}

@article{Zhang1994,
	Author = {Z. Zhang},
	Journal = {Internation Journal of Computer Vision},
	Pages = {119-152},
	Timestamp = {2008.09.02},
	Title = {Iterative point matching for registration of free-form curves and surfaces},
	Volume = {13},
	Year = {1994}}

@article{Zhao2008,
	Author = {Tao Zhao and Nevatia, R. and Bo Wu},
	Doi = {10.1109/TPAMI.2007.70770},
	Journal = IEEE_J_PAMI,
	Month = {July},
	Number = {7},
	Pages = {1198--1211},
	Timestamp = {2008.11.26},
	Title = {Segmentation and Tracking of Multiple Humans in Crowded Environments},
	Volume = {30},
	Year = {2008},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2007.70770}}

@article{Zheng2007,
	Author = {Bin Zheng and Joseph K Leader and Jessica M McMurray and Sang Cheol Park and Carl R Fuhrman and David Gur and Frank C Sciurba},
	Journal = {Med Phys},
	Month = {Jul},
	Number = {7},
	Pages = {2844--2852},
	Timestamp = {2009.05.18},
	Title = {Automated detection and quantitative assessment of pulmonary airways depicted on {CT} images.},
	Volume = {34},
	Year = {2007}}

@article{Zhu2002,
	Author = {Yang-Ming Zhu and Steven M. Cochoff},
	Journal = {IEEE Transactions on Image Processing},
	Month = {December},
	Number = {12},
	Owner = {tustison},
	Pages = {1417-1426},
	Title = {Likelihood Maximization Approach to Image Registration},
	Volume = {11},
	Year = {2002}}

@book{Zienkiewicz2000,
	Author = {O. C. Zienkiewicz and R. L. Taylor},
	Edition = {5},
	Owner = {tustison},
	Publisher = {Butterworth Heinemann},
	Title = {The Finite Element Method, Volume 1: The Basis},
	Year = {2000}}

@article{Zunic2003,
	Author = {Zunic, J. and Rosin, P.L.},
	Doi = {10.1109/TPAMI.2003.1227997},
	Journal = IEEE_J_PAMI,
	Month = {Sept.},
	Number = {9},
	Pages = {1193--1200},
	Timestamp = {2008.11.26},
	Title = {Rectilinearity measurements for polygons},
	Volume = {25},
	Year = {2003},
	Bdsk-Url-1 = {http://dx.doi.org/10.1109/TPAMI.2003.1227997}}

@book{Amini2001,
	Editor = {Amir A. Amini and Jerry L. Prince},
	Publisher = {Kluwer},
	Timestamp = {2007.09.09},
	Title = {Measurement of Cardiac Deformations from MRI: Physical and Mathematical Models},
	Year = {2001}}

@other{cdash,
	Timestamp = {2009.06.09},
	Url = {www.cdash.org},
	Bdsk-Url-1 = {www.cdash.org}}

@unpublished{sipidatabase,
	Institution = {University of Southern California},
	Keywords = {image database},
	Note = {Texture image database, available at http://sipi.usc.edu/database/},
	Timestamp = {2008.05.26},
	Title = {USC-SIPI Databse},
	Url = {http://sipi.usc.edu/database/},
	Year = {2008},
	Bdsk-Url-1 = {http://sipi.usc.edu/database/}}

@manual{NHLBI2007,
	Organization = {National Heart Lung and Blood Institute},
	Timestamp = {2007.09.08},
	Title = {Expert Panel Report 3 (EPR 3): Guidelines for the Diagnosis and Management of Asthma},
	Year = {2007}}

@manual{WHO2006,
	Edition = {Fact Sheet Number 307},
	Month = {August},
	Organization = {World Health Organization},
	Timestamp = {2007.09.08},
	Title = {Asthma},
	Url = {http://www.who.int/mediacentre/factsheets/fs307/en/index.html},
	Year = {2006},
	Bdsk-Url-1 = {http://www.who.int/mediacentre/factsheets/fs307/en/index.html}}

@manual{ATS2000,
	Journal = {Am J Respir Crit Care Med},
	Keywords = {Asthma; Bronchial Hyperreactivity; Humans; Risk Factors; Terminology},
	Month = {Dec},
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